Raising Hell
by LegionofShadowhunters
Summary: The Clave ordered the Silent Brothers to find a "cure" for Jonathan Morgenstern's demon blood so he could be raised like a normal shadowhunter after his father died. He spent his entire life training and hunting with Jace and the Lightwoods, and trying to forget his evil father. He was doing well until the little sister he didn't know he had showed up clueless about the shadowworld
1. Chapter 1

**Author's Note: This is my first fic and I don't usually write in third person so this might be a little rocky. This chapter is mainly just introducing the shadowhunters/explaining how Jon's demon tendencies are being controlled.**

 **Disclaimer: I do not own the mortal instruments or any of the characters. There are also some references to plot lines used in _Shadowhunters_.**

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The control room of the New York Institute buzzed with more activity than usual. A recent string of mundane murders had piqued the interest of the local shadowhunters. In a city as big as New York murders weren't exactly uncommon but after five victims had shown up nearly completely drained of blood the Clave had ordered they look into it.

Hodge handed out case files to the four young shadowhunters sitting at the table in front of him, the Lightwood siblings and both Jonathans. Alec, the older of the two Lightwoods, opened his immediately to study the mundane police reports. His dark hair hung down in front of his blue eyes as he scanned the documents. His sister Isabelle tied her long black hair up before diving into her own.

Hodge remembered watching Alec stumbling around with uncertain steps as a toddler and seeing the surprised look on his face when he first shot an arrow straight into the center of the target as a thirteen year old. He had a tough time training Isabelle. She hadn't been as enthusiastic about seraph blades and daggers like her brothers had been. She excelled at fighting with them but it wasn't until she had gotten her electrum whip that she truly felt comfortable using a weapon to fight. He'd seen Isabelle become a confident young woman, and Alec become a respectable leader. Hodge was probably prouder of the two of them than he should have been

Jonathan, the older one, ran a hand through his nearly white hair and flipped through the crime scene photos. Hodge tried his best to be discreet in checking the oldest boy's eyes. Jonathan's father had been infamous for his violent nature towards downworlders when he was alive, it wasn't until after he supposedly died in a fire that anyone found out about his experiments. Valentine Morgenstern had start by injecting himself with demon blood, hoping he would gain some sort of boost in his fighting abilities. When his wife became pregnant he decided to slip the blood to her in her food. He thought the effects would be stronger if the demon blood was introduced while the child was developing. The Silent Brothers worked hard to create potions and medicine to help dull the effects on Jonathan. Before the Brothers' interference Jonathan had been an unusually aggressive child, his irises were a constant black. When he took his potions and his shadowhunter blood became dominant, and his eyes would turn the same green as his mother's. Hodge hated working with Jonathan on the days he ran out of his medicine, he became angrier and more defiant. Training on those days were difficult, Jonathan would struggle with focusing on direction and would get easily frustrated when he messed up.

Today his eyes were green.

The younger Jonathan, who had been nicknamed Jace to avoid confusion when he arrived at the institute as a ten year old, flipped through the pages without really caring what any of them said. His golden blond hair was combed back and he was already dressed in gear while the others still wore their normal clothes. Jace's enthusiasm for the hunt and the fight couldn't be matched, but his reckless, impulsive nature had gotten him into trouble more times than any of them could remember. Hodge had enjoyed training Jace, he had skill and talent to spare. Being his commander was exponentially more difficult. His enthusiasm may have been admirable but it was also difficult to contain. He didn't envy Maryse and Robert's position.

"If we look at this objectively," Hodge began, "we could probably come up with a list of suspects. Maybe some of you could make use of your downworld contacts and see if you could get some extra information." He looked pointedly at Jace and Izzy. Jace didn't react, looking bored as he flipped through the mundane police file. Izzy rolled her eyes and smirked. Both of them had histories of relationships with downworlders, never anything particularly serious but enough they had established some permanent connections.

"Alright, let's start with the obvious," Alec spoke first, getting the attention of his parabatai and his sister, "Blood drained, limited to no signs of a struggle. The Dumont vampires would probably be at the top of the list. They use encanto to subdue the victims and drain them of their blood. The mundies probably wouldn't even know that it's happening."

Hodge pulled up the most recently updated stats on the New York vampires. " _Dumort,_ " Jace said. He closed his file and tossed it on the table. He kicked his feet up and leaned back in his chair. "They renamed it. Hotel Dumort."

"Hotel of Death," Izzy translated, "Can't say they don't have a sense of humor."

"The vampires wouldn't do it," Jonathan spoke up. Alec shot him a brief glare. Hodge couldn't tell if it was because his suggestion had been dismissed or if it was because Jonathan had been the one to dismiss it. The two of them had never quite gotten along. They had their moments, but for the most part Alec was the only one of the kids that held his demon blood against him. Naturally, Jonathan took a lot of offense to the fact. "Since Camille Belcourt went M.I.A., Raphael Santiago has been in charge. I guarantee you, you couldn't find a downworlder who wants to avoid The Clave more. He wouldn't allow any one in his clan violate the Accords."

Isabelle closed her file and pushed it to the center of the table. "Anything else would probably just be demonic activity. I can't imagine werewolves draining anybody's blood, and I definitely couldn't see one making that clean of a kill. The fae wouldn't have any use for the blood. I guess a warlock could. They could use some sort of spell to stun them then they wouldn't fight back. They could probably use the blood in some sort of ritual."

Hodge pulled up a list of the warlocks in New York. He flipped through the profiles and shook his head. "The New York institute hasn't had problems with any warlocks for decades. Most of them keep to themselves. A few use glamour to cover their warlock's marks and work in mundane jobs."

"Hodge is right," Jace agreed. "Warlocks are probably just as unlikely as vampires to start something with the Clave. The Circle did target them specifically for a while. They're all pretty wary of shadowhunters."

Isabelle pushed her chair away and stood up. She flashed the group a grin, "I guess it's time for me to make some visits to some of my _friends_." She turned to Hodge, "I'll be back with information as soon as I can."

"Just don't tell your parents I was the one to suggest it," Hodge begged. The Lightwoods didn't like their children associating with downworlders. He turned to Jace, "Do you have anyone you need to talk to?"

"No one that would want to talk," Jace shrugged. "I wish I had more to offer but I don't."

"Well alright," Hodge cleared his throat and collected their files, "Izzy, go collect some information. Alec, my advice is to contact the Clave and tell them we're working on it."

"Won't they get upset with me for not having anything concrete to tell them?" Alec hadn't ever been in charge of the institute during such a sensitive mission. He hadn't had to have any discussions of this caliber with the Clave until recently. Hodge still had to reassure him anytime the Clave was brought up.

"They'd be more upset if they didn't get updates. These things take time. If they give you a hard time and say you need to hurry it up remind them that New York is a big city with a large downworlder population." Hodge gave him a pat on the shoulder. "You know what you're doing, kid." He looked at the last two boys sitting at the table. "You two, training room. Bo staffs. Go."


	2. Chapter 2

**Author's Note: My goal is to update at least once a week. The only reason I'm updating two days in a row is because I already had a draft of the Pandemonium scene ready. This probably won't happen a lot sorry.**

 **Disclaimer: I do not own the mortal instruments or shadowhunters or any of the characters.**

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Jonathan hated going to downworld clubs. It wasn't so much that he didn't like downworlders—he was pretty indifferent towards them if he was honest—or the atmosphere of the clubs themselves. He hated them because it reminded him that he was technically one of them, a creature with demon blood. The older he got the easier it was to ignore it when a visiting shadowhunter would think he was out of earshot and refer to him as an abomination to another adult. As a child, however, the word had made him want to vomit.

It wasn't like he wasn't trying. He'd been doing everything, taking everything, that the Silent Brothers told him to since he was three years old. When he was younger he used to have trouble controlling some of his more violent impulses, but by the time he was ready to train he hadn't punched a wall or broken a piece of furniture in months. He actually found that the physical aspects of his training had helped him release a lot of his aggression.

Jonathan still had trouble with his emotional control. If he had taken his potion he didn't have to worry about any irrational feelings of anger. The problem was that any time he felt even the slightest bit of anger he would get twice as terrified as he was upset. He was afraid the potions stopped working, and he was afraid the demon blood had suddenly grown stronger. No matter how often Brother Zachariah told him that some anger was natural and most likely perfectly justified he couldn't shake the feeling that he shouldn't allow his mind to even go into that direction. He spent most of his time trying not to feel anything. It was easier than picking and choosing what got to stay and what had to go.

Being in Pandemonium was absolutely miserable. There were downworlders and probably some mundanes in the mix of people on the dance floor. The flashing lights and loud music were giving him a head ache and he regretted his decision to volunteer as look out. Alec and Jace had slipped into one of the backrooms and Izzy had taken her place in the center of the dancefloor. The blue haired demon boy that her Seelie friend had told her about came in right on time. The plan was going well, she had successfully lured the demon onto the dance floor and soon enough back to Alec and Jace.

Alec had objected to using his younger sister as bait which Jonathan didn't fully understand since she had volunteered. Izzy had been offended and reminded all three of them that calling her bait implied she wouldn't fight back and that she would be more than happy to demonstrate her abilities on one of them to prove herself. None of them were stupid enough to take her up on her offer.

Jonathan watched as Izzy leaned in and whispered in the demon's ear, pulling away with a seductive smile. She grabbed the demon's hand and started leading him out of the crowd and towards the back hallway. Jonathan started to follow, keeping to the perimeter of the room so he wouldn't get jostled around by the dancers. Out of the corner of his eye, he spotted a head of bright red hair, not an unnatural red like some of the club patrons dyed theirs but a true carrot top red. He realized he wasn't the only person following the couple—if you could even call them that.

He tried to move closer to get a better look at the girl. She didn't look old enough to be in here. She was too small and too innocent looking. As far as Jonathan could tell she wasn't a demon, she was pale but not the deathly pale of a vampire, it was getting close to a full moon and a young werewolf wouldn't risk turning in such a crowded place, she didn't have a warlock's mark or any signs of Fairy blood. No runes. She was just a mundane. A mundane that could clearly see Izzy.

If the little girl had the Sight and she got back to that room in time to see Jace and Alec do the angel knows what to that demon she'd be scarred for life. Jonathan had to get to her before she could get back there.

Jonathan started pushing through the crowd to get to her. He tried to think of ways to distract her so Izzy and the demon could slip away unseen. He could run into her and start apologizing profusely then she'd be socially obligated to listen to him unless she wasn't worried about being rude. He could knock the drink out of someone's hand so it splashed on her. Cleaning her shirt might be enough to get her to forget Izzy and the demon.

She was able to slip into the hallway before he could reach her. By the time he reached the hallway, it was empty. Maybe she was just looking for a bathroom and got lost. Jonathan looked around to make sure he was alone and backed up towards the door his friends were behind.

He heard the struggle before he saw it—The demon lashing out against Alec and Jace as they restrained him, Izzy snapping her whip more as a threat of pain then to actually dish any out. Jonathan pulled a Seraph blade from his belt and muttered the name of an angel. The sword glowed as he joined the other three.

"Tell us who you've been working for," Jace growled as Alec tightened the electrum around the demon's wrists. Black ichor dripped on the cement floor and Alec's boots.

The demon grinned. "Wouldn't you like to know Nephilim," It mocked. It had a nasally voice that made it seem more annoying than threatening.

Jace pulled his fist back and slammed it against the side of the demon's jaw. "Look," Jace's voice was even and reasonable but the threat was clear, "Either you tell me and I let you die fast or you don't tell me and the four of us will take turns slicing you open until you're completely drained, just like those mundies."

It didn't seem scared, amused but not scared. "You wouldn't believe me if I told you," It laughed and Izzy snapped the whip so it cut against its leg. The demon hissed and gritted its teeth together. "You Nephilim are too arrogant and blind."

Jace pulled out his own Seraph blade and dragged the tip down the front of the demon's shirt, applying just enough pressure to draw blood. Ichor spread from the center of the demon's chest. It grinned and whispered, "You want a name? Valentine. Valentine Morgenstern."

Jonathan's grip on his Seraph blade tightened. _He's dead. He's dead. He's dead. He's dead._ He thought he was going to throw up. His father had died in a fire that was meant to kill him. Valentine had tried to burn Jonathan alive when he was only two years old. When shadowhunters had spotted the fire and ran in to find Jonathan and his family they had found him first and was able to save his life. There wasn't a shadowhunter or downworlder alive that hated Valentine more than his own son.

Something came crashing down near the door, distracting the demon and shadowhunters from their interrogation. The red headed mundane girl had fallen in front of the door way. She looked shocked at first but scrambled to her feet, regaining some confidence and composure. "Let him go," She ordered, "You can't just torture people for information."

"This," Jace gestured towards the demon, "Is not a person, Red."

"Jace," Alec hissed a warning to his parabatai.

"Jon, take her out of here," Jace instructed. Jonathan stepped forward and grabbed the girl's arm. He didn't want to hurt her but he was afraid she'd fight back, "We'll take it from here." Jonathan was more than happy to get away from the demon.

He pushed the girl out the door, ignoring her protests, but she decided to fight back just as Jace drove his Seraph blade through the demon's heart. The girl screamed and Jonathan looked over his shoulder. Ichor sprayed against Jace's gear, some of it staining Izzy's white dress, and the demon dropped to the ground, slowly dissolving into nothing. It was a normal sight for shadowhunters, a mundane would go into shock.

The girl took advantage of Jonathan's distraction and twisted out of his arm and ran for the emergency exit of the club. Jonathan made it out just as the door to her cab was closing. He focused on the girl's voice and with the boost his hearing runes provided him he was able to make out part of her address. The cab sped away before the other's found Jonathan standing alone on the side street.

-o.0.o-

When they got back to the institute Alec met with Hodge to discuss what he should tell the Clave about their mission. They were all shaken by the mundane girl and the mention of Valentine. It was hard to decide what the Clave needed to know about the night's events. Izzy had gone back to her room to change into something without ichor splattered all over it. Jace and Jonathan had gone to the weapons room to put back anything they didn't use and clean whatever they had.

"Do you think we should check up on that mundie girl?" Jace asked when Jonathan handed him a set of throwing knives to put away.

Jonathan grabbed a couple unblessed Seraph blades and went to hang them up on a rack. "I don't know. Do we really have a reason to? If she says she saw anything they'll probably put her in therapy or something. No one would believe her."

"Yeah but, the downworlders at Pandemonium could have seen her follow us. We should at least check on her to see if she was followed or tracked or something." Jace leaned against one of the tables and twirled his stele between his fingers. "I wouldn't even know where to start to look for her and Alec would never let me near any of the files of mundies with the sight."

The street name Jonathan overheard came to mind. "You just want to check on this girl? Make sure she's safe?" Jace nodded, staring blankly at the wall. He was probably thinking about ways to get around Alec and see if he could find anything about the girl in the institute's files. Jonathan wasn't even sure if the Clave kept record of that kind of thing. Jonathan squeezed his eyes shut. "If you don't tell Alec I'm the one who told you, I heard the street she gave to the taxi driver."


	3. Chapter 3

**Author's Note: I had a snow day and an essay I was supposed to be writing that I'm still not done with, so oops?**

 **Disclaimer: I do not own tmi/shadowhunters or the characters.**

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Stress weakened the effects of Jonathan's medicine. Stress involuntarily opened up his mind to the darker parts of him. Some parts made him hostile, others made him hate himself more than normal. He found the best way to deal with it was to train. He could put his aggression into a punching bag and focus his thoughts on perfect technique and counting hits.

He'd been on edge since he let Jace go off after the girl alone. They made a deal: Jace wouldn't say where he found the girl's address if Jonathan didn't tell Alec or anyone else where he was going until he got back.

 _You shouldn't have let him go alone._ Jonathan nailed a solid kick into the side of the punching bag. _If something happens to him it's your fault._ A punch so hard the entire thing rocked and he could feel it all the way up to his shoulder. A few more rapid blows and the voice in the back of his head quieted around the same time his knuckles started to ache.

"Hey Morgenstern," Jonathan flinched at his own last name and spun around to see an agitated Alec marching towards him, "Where's Jace? Hodge wants to talk to him about Pandemonium."

"Haven't seen him since the weapons room," It was true, Jonathan had stayed back to finish putting things away when Jace had left him. "Did you try his room?" He figured the least he could do was offer a suggestion even if Alec had already checked.

"I did, he wasn't-"

"Hodge! Alec!" Jace's distraught voice carried from the main entrance to the institute. It took both boys less than a second to react. They both sprinted down the hall, passing the shadowhunters working in the control room and straight to the front doors.

Wind from the thunderstorm raging outside pushed the door open before it could shut all the way. Jace fell to his knees just inside the threshold, the red headed girl limp in his arms. Both of them were dripping wet from the rain. Jace wouldn't have been able to take an unconscious mundane on a subway or in a cab without drawing attention, especially with the vicious, swollen gash on her neck.

Alec knelt down to help Jace lay her gently on the floor while Jon jumped over them to shut the door and secure the institute. The wind blew rain straight into his thin training shirt, darkening it with drops of water. "Did someone follow her?" Jonathan asked as he rejoined the other two. He figured the secret was out now that Alec had seen the girl. Alec was smart, he'd be able to put two and two together and end up with four.

Jace shook his head. "It was waiting for her. The address you overheard wasn't her house, it was someone else's. She was leaving when I got there and I followed her to her apartment. I followed her into the building but I didn't follow her upstairs. After a minute I heard a loud crash and screaming. When I ran up she was putting up a fight but she didn't have a weapon and-"

Alec held a hand up to silence his rambling. "What kind of demon? Hodge might have an antidote already made."

"Ravener."

"What's going on?" Jonathan turned his head as Hodge jogged to them. It wasn't until he was a few inches away from their group that he froze. He muttered something under his breath Jonathan didn't quite catch.

Alec must have heard because he looked up at their tutor with furrowed eyebrows. "Who's Jocelyn?" The sound of the name sent ice through Jonathan's veins. He'd rather someone sit him in a room and read him detailed descriptions of one of his father's journals than say that name.

Jonathan didn't remember a thing about his mother even if he did that fact she had abandoned him and left him with the father that was attempting to kill him would have tainted any image of her. He was a defenseless toddler and she had left him to die. He had assumed Jocelyn had died, that Valentine had killed her too. "You don't think," He turned to Hodge, his thought trailing off.

Hodge stared down at the limp girl. "She's Jocelyn's daughter, no question. She used to look exactly like that." Hodge ran a hand over his face. "Get her to the infirmary. I'll see what I can do."

-o.0.o-

Jonathan took his turn like everyone else watching over the girl for the next three days. Hodge went back to his normal work at the institute while the young shadowhunters watched over her. They took two hour long shifts to sit in the room in case she woke up.

Jace stuck around more often than he needed to. "When was the last time you slept?" Jonathan asked as he dealt out another game of War. He didn't mind having Jace there, in fact he was a good way to pass the time.

"I sleep and eat and shower in the middle of shifts, don't worry about me." Jace shook his head as he lost the first round. "So, do you think she's like your sister or something?"

"According to Hodge," Jonathan took the cards he won, "She's my mother's daughter which would have to make her my sister. I just wish I knew if she was the monster's daughter too."

They flipped their cards over and two sevens peered up at them. They laid out three cards, face down, before flipping over another one. "You don't think he-" Jace trailed off. Neither one of them wanted to hear the words out loud.

"No," Jonathan answered quickly, "She's probably around Izzy's age. So that's a three year difference between us, he tried to kill me when I was two. He probably didn't know that Jocelyn was even pregnant. And even if he did, if he was willing to kill me because of the effects do you really think he'd do it again? Besides if she showed even half of the symptoms that I did she'd probably be locked up some place." What he didn't add was that their mother probably would have ditched her.

Jace collected his giant win. They played a couple rounds before either of them spoke again. "Do you think that could have happened to you?"

"Still could," Jonathan was realistic about his status with the Clave. If he made a mistake large enough to cause Clave interference he'd probably be locked up.

The girl grunted and shifted on her bed. She'd been doing that a lot in the last day. The venom and the antidote were both wearing off now. They both looked over to see the girl rubbing her eyes and trying to kick off the thin sheet covering her legs. Jace and Jonathan both sprung up from their stools, card game forgotten.

"Well look who decided to join us," Jace plastered his signature smirk onto his face and strolled over to the end of the bed. "How'd you sleep?"

Jonathan hung back, shoving his fists into his pockets. The girl scrambled into a sitting position, with her back flat against the metal headboard. Her curly red hair was flying in all sorts of different directions and her clothes were still torn up from the demon attack. She didn't look intimidating. Jonathan took a couple steps forward. "You were at Pandemonium." Her eyes turned on Jonathan and he stumbled back the two steps he had been brave enough to take. He hadn't been able to see her that well in the lights of the club but she had his eyes. It was the same green that left him relieved when he looked in the mirror. The green that reminded him he didn't have to be a monster. On her it made his stomach twist. "You tried to kidnap me," She accused him. "What the hell am I doing here? What did you do to me?" She turned back to Jace with her questions, Jonathan's blank stare had probably unsettled her.

He looked at her and all he could think of was what Hodge had said the other day. This girl was supposedly an exact copy of his mother. They shared a parent shouldn't they look alike? She had orange freckles sprinkled across her cheeks, Jonathan knew he had faint freckles across the bridge of his nose but nothing nearly as noticeable as hers. She had high cheekbones like he did but her cheeks were fuller. Jonathan assumed that the demon blood had something to do with it. Somehow it made his cheeks hollow and slightly sickly looking. Even though the girl was a lot shorter than him, she still had a similar lanky build that he had. They didn't look as much alike as Alec and Isabelle did but there was definitely a resemblance now that it was pointed out.

"I'm going to go tell Hodge she's awake," Jonathan said quickly and turned to leave.

"Wait," Jace called. Jonathan turned his head. "Don't you want to introduce yourself, Jon?"

"I think you just did for me." He had to keep himself from sprinting out of the room.

-o.0.o-

Jonathan ran back to his room and locked the door behind him. He stumbled to the bathroom and fell to the floor by the toilet, wincing when his knees hit the tiles. He felt like he was going to throw up. His mother was alive. He had a sister. The demon at Pandemonium said his father was alive. When the Clave found out he'd be taken away, right? If the rest of his family was alive it would only be logical to take him in and question him?

It took the thought of being thrown into one of the cells deep in the city of bones to get him to start retching. Who knew how long they would keep him there? Until they caught his father? Would they do the same to his sister?

He pushed himself up onto his feet and fell into the sink. He held out one hand, using the other to support himself, his fingers were shaking and nothing in his body felt stable. It wasn't like when he skipped a dosage. Then he just felt awake and powerful. It wasn't entirely unpleasant but there was always this feeling in his bones that made his body ache a little.

He turned the cold water tap on and splashed as much as he could on his face. Someone started banging on his bedroom door just as he was getting his breathing even. "Jon!" Isabelle. "Are you okay?"

He didn't bother to towel off his face and went to let Isabelle in. "She woke up," Jonathan said it like it should have been the answer. Isabelle's eyes widened in surprise. Clearly Jace hadn't gone to spread the news. In the back of his mind he remembered he was supposed to tell Hodge. "She woke up and she freaked out because she recognized me and Jace and I freaked out because she has _my_ eyes which means I have my mother's eyes. I have a sister Isabelle. A sister that came out of thin air. _And_ that demon said my father was alive. This doesn't look good for me. Or her."

Something flickered in Isabelle's dark eyes that Jonathan recognized. The Lightwood siblings didn't make a move without knowing exactly what would happen to the other. They were fiercely protective of each other no matter how much it annoyed the other one. It took Jace's interference for Alec to be okay with letting Izzy hunt with them and Izzy spent most of her time mediating arguments between Alec and their father. Seeing Jonathan so flustered over a something like a sister triggered her feelings not just for Alec, but for Jace and Max, their younger brother, as well.

"The Clave will not take one demon's word for it that Valentine is back," Isabelle promised, "Jocelyn Fairchild's sudden reappearance into the shadowworld and the fact she has a daughter might complicate things but I don't think you're in any danger. If you were we'd all be able to testify on your behalf."

The words weren't as comforting as either one of them hoped they would be. Maybe the Clave wouldn't investigate the lead towards his father but Jace had said the girl's mother—Jonathan's mother—wasn't in the apartment. Jace, Hodge, and the Lightwoods could testify for him all they wanted but they wouldn't be able to testify for his sister. Jonathan leaned his forehead against the doorframe.

"Izzy, Jon," Alec stepped behind his sister in the doorway. "We have a problem. The little girl—Carly or whatever—says she remembers the demon saying something about a cup. Like _the_ cup. She had no idea what it was talking about, of course. Jace was trying to figure out if she knew anything about the shadowworld when I left. She was totally clueless."

"Wait," Isabelle stepped aside so she could look up at her brother, "The mortal cup has been missing for years—"

"Twenty-two," Jonathan knew the exact time because his father had been the one to steal it.

"Right, and a demon attacks her for it? Why?"

Alec looked at the top of her head for a split second then back down at her. "If I had to guess, I'd say her mother has it—Sorry, your mother." He flashed Jonathan a bitter smile that made it seem like he was blaming Jonathan for this whole situation.

Valentine may have stolen the cup but it was Jocelyn who hid it.

Jonathan straightened up and pushed his wet hair out of his face. "Tell Jace not to push it," He wasn't sure which one of them he was ordering and he really didn't care, "I'd like to talk to her before this gets too far."

"Too late," Alec scoffed, "I ran into Hodge on the way here. He went to call the Silent Brothers."


	4. Chapter 4

**Author's Note: This chapter was so awkward to write. I just couldn't figure out how to do it. I promise Jon and Clary's relationship will get less weird and tense. This is unedited so I'm sorry for any spelling/grammar mistakes. I will try to update as soon as possible!**

 **Disclaimer: I do not own TMI/Shadowhunters or any of the characters.**

Jonathan was used to the Silent Brothers, he had to see them every two weeks for the last twenty years. He knew most of the once that worked in the New York branch by name. Most shadowhunters feared the Silent Brothers for their appearance. Bald heads and stitched up mouths and eyes.

Jonathan had seen worse. Which is why he didn't hesitate in approaching the Brother standing in the hall outside the infirmary like the Lightwood siblings, in fact he was kind of relieved to see who it was. "Brother Zachariah," He greeted with a slight smile. Zachariah was his favorite Brother to deal with and the one who took the most responsibility and concern with Jonathan's condition. He had been the one to defend Jonathan to the Clave when he was barely two years old. "I was just about to come and visit you."

A visit isn't exactly what he was going to the Silent City for in a couple of days. _There will be no need._ Zachariah's familiar voice echoed in Jonathan's head. He knew Isabelle and Alec couldn't hear. He reached into his parchment covered robes and pulled out a familiar small wooden box that looked a little like a trunk carved with runes. Zachariah held out the box from an intricate metal handle. _I assumed you would be running low._ Jonathan took the box gently and vocalized his thanks.

"Did you come alone to see the girl?" Jonathan asked.

 _I did. Clarissa is your sister Jonathan. I have known her as long as I have known you. I promised your mother I would keep her identity and existence a secret. Valentine and the Clave would have been searching for both of them._ It was hard for most shadowhunters to hear anything besides a monotone drone from a Silent Brother but Jonathan liked to think he could hear a little emotion now that he'd been around them so often. He thought he could hear a little bit of an apology in the words echoing in his head. Sorry or not, it bothered Jonathan that he had known something as crucial to his life as a mother and a sister and kept it from him. _Jonathan and Hodge would not let me enter until you arrived._

That caught Jonathan off guard. He had run out of the room about forty-five minutes before he wouldn't have thought Jace _or_ Clarissa would think he was necessary for a meeting with a Silent Brother. It took him a moment to understand. Jonathan was the one that knew the Silent Brothers better than anyone. If anyone could possibly make it easier it would be him.

"I'll go in and talk to her," Jonathan looked Brother Zachariah up and down, "No offense but she's going to need a pretty big warning before you come walking in."

He didn't stick around to hear Zachariah's two cents. He opened the door to the infirmary just enough for him to squeeze through. Jace and Clary were talking quietly on her bed but in the large empty room their voices seemed to echo. Hodge was standing at the counter putting bottles and containers of ingredients back into the cabinets. They turned their heads as the door clicked shut behind Jonathan. "Brother Zachariah is here. I told him to give us some time so we could prepare her."

Hodge looked up from what he was doing. "I should go greet him. I need to go check on Alec and the control room anyway." He left without another word.

"Prepare me?" Clarissa turned to Jace for an explanation. "For what?"

Whatever Jace had done after Jonathan had left it clearly made the girl trust him and his judgement. It wasn't until Jace addressed Jonathan directly that she turned her anxious eyes on him. "She doesn't know anything, Jon. She's definitely a shadowhunter but she didn't even know what the word meant." Jonathan had been wondering why the Silent Brothers need to be called to the institute. The best way to figure out what was going on in her head would be to ask someone who could read minds.

It probably shouldn't have surprised him that she didn't know anything especially with how flustered she was when she woke up. Jonathan walked to the bed and stood a few feet to the side. He set his box of medicine on the side table of the next bed in the infirmary. He crossed his arms over his chest and looked at a spot just above his sister's head. "Jocelyn didn't tell you anything?"

"She didn't know about you or your father," Jace answered.

"I can speak for myself," She protested before turning to Jonathan. Once again he was taken aback by seeing his own eyes set in someone else's face. Alec and Isabelle didn't even have the same eye color. "Look, I had no idea you existed and judging by your reaction to me I'm guessing this is news to you too. My-our mom is gone and I don't want to deal with this Silent Brother guy unless I know that this can help me find her. I can't waste any time."

Jace looked between the two of them with a worried expression. Most of the shadowhunters at the institute handled Jonathan with an obnoxious amount of patience and wariness. Clarissa didn't know about Jonathan's demon blood and she didn't seem like the type of person that would care either way. If she was annoyed with you, you would know it. Jonathan respected that. He was sick of having everyone tiptoe around him.

"Look, I didn't know Jocelyn," Jace sucked in a deep breath at the bitter edge to Jonathan's tone, "She may have given birth to me but she's your mother not mine. I don't know how she blocked your sight and kept you from the shadowworld but Brother Zachariah might be able to help you. Maybe it helps find your mom maybe it doesn't but it's worth a shot." Jonathan didn't want to say what he really thought when she said their mom was gone. Jocelyn had abandoned one child why not two?

Something he said brought a look of hope to her face. He had tried to remain as neutral as possible to prevent this type of reaction. "You know why though," She accused. "You said you didn't know how, but you didn't say you didn't know why."

Jace and Jonathan exchanged an awkward look and Jonathan knew they had come to the same conclusion. Jocelyn had kept the shadowworld away from Clarissa because of Jonathan and Valentine. There would be a lot of disgusting truths to face if she knew the truth. Jonathan looked back at his sister and sighed. "Trust me when I say you don't want me to tell you."

Clarissa shifted to the edge of the bed like she was ready to stand up. "You don't even know me. I _do_ want to know." Something her tone made it sound like a dare. It was a good thing it was directed at Jonathan instead of Jace. Jace took any challenge or dare personally and refused to back down. Jonathan didn't have a problem with letting it roll right off his shoulders. "Considering my _entire_ life has been hidden from me I think I deserve to know why."

"No, you don't." Jonathan said carefully. He didn't say that she didn't deserve to know was because she had done nothing wrong. She clearly cared for her mother and looked up to her. She didn't deserve to hear about her mother's questionable past from anyone but Jocelyn herself. Jonathan's version would probably be too bitter and venomous to pass for unbiased and Jace didn't seem to think it was his place to talk about their family.

She turned on Jace and gave him a small smile. "You're the one who thinks I should know about where I come from, don't you think I should know about why she kept this from me in the first place?" Jonathan had seen Isabelle use the same technique on many unsuspecting targets. Batting eyelashes and a shy smile could do wonders when turned on unprepared men. Luckily Jace was used to female attention and only seemed happy that she was noticing him and not fooled by her flirting.

Jonathan wasn't going to take a chance. He didn't look away from his sister when he said, "Jace, you should leave. Wait outside with the others. I'll come get Brother Zachariah when we're ready." The other boy hesitated for a moment before taking Clarissa's hand and giving it an apologetic squeeze.

"Is Alec outside?" Jace asked as he stood up. "I need to make sure he isn't still pissed at me."

"Yeah. I wouldn't worry about Alec, he's always pissed."

Jace stretched his arms over his head and yawned on his way to the door. "He needs to get laid."

Jonathan scoffed and watched as the doors to the hallway shut. "My name's Clary, by the way, since you didn't ask me." The sound of his sister's voice turned his attention back to the task at hand.

Jonathan sat on the edge of the bed like Jace had but perched closer to the end. "Jon. Nice to meet you. Wish it could have been under better circumstances." His voice sounded hollow to his own ears but he knew he meant it. It stung knowing she probably wouldn't.

He'd spent his entire life watching the way Isabelle looked up to Alec and the way Alec protected Isabelle. He'd spent just as much time envious of their relationship. There was so much unconditional support between the two of them, support Jonathan couldn't fathom.

He knew there wouldn't be any way for him to get that close to Clary, the trust between the Lightwoods had been there since they were toddlers, but he wished he could. He had a chance to support someone the way Alec did.

"I want you to know you can trust me," He said slowly, choosing his words carefully, "You can ask me anything but if I don't answer it's for your own good, please believe me." He was more successful at having some sort of emotion in his voice this time around.

"So you're saying you're going to lie to me but I should trust you," She raised her eyebrows in disbelief.

Jonathan shook his head and rested his hands on his knees. "No, I'm saying that there will be things I'm not going to tell you for your own good."

Clary leaned back on the pillows and pulled her legs back up on the bed. "Are you sure you don't know Mom? Because you two seem to have similar views on what's good for me." They both knew it was a cheap shot but Jonathan decided it was fair.

"How about this," Jonathan didn't know why he was trying to bargain with her, probably because he knew deep down this was a chance for him to have a family, "If you do everything Brother Zachariah asks I will answer three of your questions as long as it's not about why I think Jocelyn kept you out of the shadowworld."

"Any question?" She looked up at Jonathan skeptically, but he nodded. "You'll answer?" He nodded again and could feel a small smile make its way onto his face. "Can I ask one now?"

The surprised him. Clary was smart, she had been able to catch that Jonathan didn't say anything about knowing about their mother's motives and she had known that there was a reason he hadn't mentioned it. And she was definitely curious if she was willing to press her question. Jonathan had told her that Brother Zachariah would help answer her questions, she had to know that if she asked a question know she risked wasting it. If it could avoid an uncomfortable conversation later, he wouldn't protest. "Go ahead."

She pointed to the box resting on the side table. "You were holding that weird, what does whatever in it do? Is it some powerful shadowhunter thing?" His nausea returned from earlier. Maybe he wouldn't be able to avoid uncomfortable questions afterall.

Clary didn't know anything about Jonathan's demon blood, she wouldn't have the same bias other shadowhunters had towards him. Jonathan knew he'd be risking that the second he told her. He also knew that if he went back on his promise seconds after giving it he could consider her trust gone. The latter definitely seemed worse.

He sighed and gestured for her to hand her the box. Clary picked it up and handled it with the same care Jonathan had when he walked in the room. She set the box down in between them. Jonathan stared at the symbol of the brothers engraved on the top. He tried to convince himself this really was a good idea. If she knew the severity of the situation maybe it would help him gain her trust. "This isn't easy," It was a lame start and he knew it, "I've never had to admit this before, everyone just _knows._ It was kind of a big deal when they found me." Clary tried to speak but he shook his head to shush her.

"This is my medicine—potions made for me by the Silent Brothers. When Joce—our mother was pregnant with me my father fed her demon blood. He would slip it into her food. He was," Jonathan paused to pick the right word and to collect his thoughts. Explaining was harder than he thought not just because of the anger bubbling in his stomach, but because of the fact he's never had to explain before. " _Curious_ about the effects. You know how when a pregnant woman drinks alcohol the baby can have a wide range of defects? That's kind of what happened. I was—am more aggressive than a normal person.

"Brother Zachariah convinced the Clave, our government," He added incase Jace hadn't gotten to that part, "That the Silent Brothers could create a cure or at least a way to help control it."

With shaking hands, Jonathan opened the box and exposed the new syringe and needles and vials of the dark purple potion. A folded piece of parchment was stuck in the lid but he ignored it. "I have to inject myself once a day. If I skip one I'm an entirely different person. I'm usually pretty good at remembering to take it sometimes when I'm busy I'll get low and forget to go pick up more. Then I'm intolerable until someone can get more for me. Even though the Brothers terrify him, Jace usually volunteers. I get locked away in my room. It's," He hesitated and whispered the last words, "Dangerous to let me out in public when I skip dosages."

"Besides," He let his voice go back to normal volume as he shut the case and pulled it into his lap, "It makes me too sick to be off of it. I go through withdrawl."

"Jon," Clary said softly, "I'm so sorry." He hadn't been expecting that reaction at all.

Jonathan shrugged it off, the sooner this moment was over the better. "Look, it's important you know that the Silent Brothers look pretty gruesome. They look terrifying but they are trying to help you. Brother Zachariah told me in the hallway that he knew your mother _and_ about you. He wanted to protect you. Remember, this guy was on my side and Jocelyn's. You can trust him."

Clary straightened her shoulders and nodded once. "Once last thing," Jonathan promised, "The Silent Brothers are called silent for a reason. They don't speak. They can't. They communicated through minds. He'll be able to see your thoughts and your memories and he'll be able to speak to you that way. It feels a little weird and invasive but it shouldn't take long. I have to take my medicine back to my room but I'll send Jace in with him, okay?"

Jonathan could feel guilt welling inside him at the idea of leaving her alone. "I still get my two questions right?" He looked up at her and the brave look she had on ten minutes ago was gone. She looked like the little girl he had seen in the club again.

He gave her a smile he hoped was reassuring. "I promise. I'll come by and get you later after Zachariah and Hodge clear you."

He left and sent Brother Zachariah and Jace in. Alec and Isabelle had disappeared with Hodge to run the institute.

Jonathan set the new wooden box on top of his dresser next to the one that was still half full. He remembered the parchment stuck in the lid and opened it up. He hadn't had a note in one of his boxes since he first started giving himself his own injections. Even then it was only step by step instructions written in neat handwriting. It had been years since then. He slipped the noted out and flipped the heavy parchment over. Three names were written in Brother Zachariah's neat handwriting.

Magnus Bane

Catarina Loss

Ragnor Fell


	5. Chapter 5

**Author's Note: So my laptop has started making weird noises. I put what I have written on a flash drive just in case but if I don't update at least once a week it's because my computer is most likely getting repaired. Again this is a long/awkward chapter but I needed to get it done. I love hearing feedback so please review.**

 **Disclaimer: I don't own tmi/shadowhunters or any of the characters.**

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Jonathan knew by the last names that they were warlocks, he'd just hadn't heard of two of them. Magnus Bane was the high warlock of Brooklyn. He kept out of the way of the shadowhunters and skirted around the Accords on the regular. For whatever reason Robert and Maryse never told Jonathan and the others to look into any of his more noticeable infractions.

The other two either weren't influential enough for the New York conclave to pay attention to them or weren't locals. The only way to know for sure was to look it up on one of the institute computers. Just because the New York shadowhunters weren't in contact with them didn't mean other institutes hadn't done any business with them.

Going to the control room would complicate things. Alec and Hodge were probably working in there and he couldn't risk wandering eyes and curious questions. There was a lab in the institute's basement used for autopsies that had a couple computers. The odds of anyone using that room were slim and even if he did no one would deny him a quick fifteen minutes to look up the names and write down some background information.

He could be in and out with minimal interference. Jace was with Clary, if she wanted to talk to him Jace could call him and find him. He folded the piece of parchment back up and tucked it into his pocket. Jonathan crafted a lie about needing to retrieve some files from the mundane police stored down in the labs if anyone asked what he was doing. He was still technically working the case with Jace and the Lightwoods they just had a little bump in the road.

The lab was a cold concrete room that lacked the same intricate architecture as the rest of the institute. There was a line of thin windows at the top of the outside wall. There was a thick layer of dirt on the outside of the glass that prevented any natural light from getting in. The room was empty and both computers were off. Jonathan figured that since the only cases they were working on with body counts involved mundane deaths the shadowhunters weren't given access to the bodies. Whatever the mundane police reports showed, the shadowhutners would have to take their word for it.

It didn't take long for Jonathan to confirm what he knew about Magnus Bane. High warlock of Brooklyn. Liked to party. Powerful downworld allies although he never used them. He had helped fend off The Circle when they made a stop in New York shortly after Jonathan was born. It made him sick to know that he was alive at the same time his parents were doing such awful things.

There didn't seem to be anything interesting about Catarina Loss. She worked as a nurse at a hospital in Brooklyn. There were some records of a friendship with Magnus Bane and Ragnor Fell but she was more of a passive participant of the events than actively seeking out trouble.

Ragnor Fell turned out to be the high warlock of London. Other than his friendship with the first two on the list, Jonathan couldn't find any reason he'd have business in New York.

Maybe they knew about Clary and their mother too. Jocelyn wouldn't have been able to escape this long with only Brother Zachariah's help. He wouldn't have been able to leave the Silent City at just any time, the warlocks on the other hand didn't have the same limitations. Jonathan still had his doubts if his mother's most recent disappearance was voluntary or not. He'd have to see Clary's apartment before he made any judgements. Jace had filled out the report and said it had been destroyed. There were obvious signs of struggle according to Jace, but that could have all been from Clary and the demon as easily it was from Jocelyn and whatever she was fighting against.

His phone buzzed in his pocket and he held it up to his ear without checking the number. "What's up?" The only people who ever called him were Jace and Izzy so he wasn't worried about formalities.

"Jon, where are you?" Jace's voice sounded slightly irritated as it came through the phone. "Clary's on the phone with some friend of hers right now but she wants to talk to you."

Jonathan switched his computer off and slipped the paper back into his pocket. "I was, uh, just checking on a couple files. Where are you guys? I'll come to you."

"I'm leaving her in the study I have a job I have to give Izzy real fast but I'll meet you in there." Jace hung up before Jonathan could respond.

Jonathan stopped by his room to grab a heavy army jacket he wore when he went out without glamour. The collar was high enough that concealed the runes on his neck fairly well and the rest of the jacket was baggy enough that he could tuck a couple knives into the inside pockets without raising mundie suspicions.

He'd be able to convince Jace to take him to Jocelyn and Clary's apartment—or what was left of it, but he doubted he could get Clary to stay behind. If Jace and Jonathan were with her she'd be as safe as she could get. Alec would probably want them to keep her in the institute but she'd probably go insane. Sure she'd be safe but she wouldn't have anything to do.

When he got to the study Jace had already gotten back. Clary was sitting on the floor by an outlet, her phone plugged into the wall and sitting on the floor beside her. Her head was tilted back against the wall and her eyes were squeezed shut. Jonathan used to get headaches after the Silent Brothers riffled around in his brain, he couldn't imagine the migraine she had right now. Her hair was wet and she was wearing some of Isabelle's more modest clothes. Jonathan didn't think he'd been in the basement long enough for her to shower but maybe he spent a little more time trying to find the warlocks' importance than he had thought.

Jace was sitting in one of the chairs with his stele in his hand. He was using it to tap out a rhythm on the arm of the chair. "How'd it go?" Jonathan slid into a chair across from him, keeping his voice low.

Jace stared blankly at the floor in between them. "Brother Zachariah was in her head for maybe twenty seconds before he hit a block in her memory. We did find out one thing though," Jace met Jonathan's eyes and put on a bitter smile, "You share both parents."

Jonathan's stomach sank. There wasn't any signs that Clary had the same _illness_ as Jonathan, but that didn't mean he hadn't done something to her. "Damn it," Jonathan hissed and fell back into his chair. He buried his face in one of his hands. "Was he at least able to find out who put the block on her mind?"

"MB." Jace and Jonathan both looked over at Clary who was staring at both of them. Jonathan got the feeling she didn't like being talked about like she wasn't in the room. He understood the feeling. He spent most of his childhood listening to adult shadowhuntes argue about his status as Nephilim. "Jace said it was some guy named Magnus."

The note in Jonathan's pocket felt like a weight. "I guess if anyone would be able to put a block on your memory and your sight it would be a warlock."

"It's not on her sight just her memory," Jace corrected, "She saw us at the club when we were fully glamoured. It makes her _forget_ anything from the shadowworld."

Clary got up and perched on the arm of Jonathan's chair. He instinctively moved as far away from her as possible and regretted it the second she saw the apologetic look on her face. She hadn't meant to startle him, and she hadn't, he just wasn't used to people getting so close to him. "So what exactly are we going to do about this warlock guy? I'd like my memories back."

"I've got Izzy looking for ways to contact Magnus Bane. He doesn't like the shadowhunters so it might be difficult. Besides we have more pressing problems to deal with," Jace said, looking pointedly at Clary.

"I'm sorry. What did you want me to do? I haven't been conscious for the last three days—he hadn't heard from me in three days. He's not going to believe I'm fine unless he sees me." Clary fired back.

Jonathan looked between the two of them. "Am I missing something?"

Clary crossed her arms and looked down at him. "My best friend Simon left me like a hundred messages while I was out. I called him to tell him I was fine and that he shouldn't call the cops. He wanted to meet with me to make sure I wasn't lying to him. I told him I'd meet him for coffee in an hour and Jace flipped out."

He knew his sister was looking for him to take her side, but in this instance he couldn't. Jace had every right to freak out. For starters she'd probably insist on going alone, which would earn her a big fat no if she even tried to ask. Then there was the fact they didn't have time to prepare a backstory and the mundie would certainly ask questions. "And what are you going to tell your mundane friend when you see him?" Jonathan raised an eyebrow in question. "That you and your mother are part angel warriors and that she kept it from you your entire life and you found out because a demon attacked you and another part angel warrior saved you? Clary, I _am_ one of the part angel warriors and I think that sounds crazy."

"No," She said even though it sounded a lot like that was close to her plan, "My mom told me her and my dad were never married and that he died before I was born. I'm going to tell him that you tried to find your dad after he left when you were a little kid and found out about me and that you wanted to meet me."

At least she had a plan B for when the inevitably denied her from telling the mundane anything, even if it wasn't completely solid. "That doesn't explain your mother's disappearance or yours," Jace pointed out, "I honestly doubt two long lost siblings would go three days without learning a thing about each other."

Clary looked deflated. "Why can't I just tell him the truth? He's _Simon_."

"You say that like it's supposed to mean something to us," Jonathan noted. Whoever Simon was he clearly was important to Clary but that didn't mean Jonathan and the other shadowhunters should trust him. "Look, we will go to meet your friend—all three of us—and we'll give him whatever story he seems the most likely to believe. Our resemblance is undeniable once you point it out, he'll have to believe I'm your brother."

Clary stood up and turned to face Jonathan head on. "He'll only believe the truth. He grew up on _Harry Potter_ and _The Lord of the Rings_ , I honestly doubt shadowhunters will be too hard to believe." Jonathan looked around her to Jace who seemed equally confused by the references she had made. They didn't really have time to get into mundane pop culture. "How could he think I was making it up with you two right there?"

Jonathan knew that even with his jacket covering most of his runes his skin was pale enough that it made the dark marks even more eye-catching. A mundane he passed on the street wouldn't notice them but one sitting across from him for more than five minutes would have enough time to see them and ask questions.

"Besides," Clary pushed on, arms crossed over her chest and a triumphant smile spreading across her lips, "Our most notable similarity is our eyes—our _mother's_ eyes. Simon has known me and Mom since I was six years old, I think he would have noticed if I had a brother."

Jonathan matched her smile and tilted his head to the side, "Why would he? You didn't." She glared at him and, oddly enough, Jonathan was thrilled. It was the kind of look Isabelle gave Alec when he pointed out a mistake in her reports. It wasn't much in the way of bonding but any similarity between their relationships was enough for him.

"I think we should tell the mundie," Jace's easy voice got both of the siblings' attention. The incredulous look on both their faces was enough to get him to elaborate, "If she's going to fight this hard to tell him she _will_ tell him it's just a matter of when. Save us the trouble and just tell him today. I'd rather just deal with the consequences than try to avoid them."

Jonathan and Jace had similar views on the Clave, they complicated things and got in the way of the real work that needed to be done, but even Jonathan knew this wasn't a good idea. He stood up and shrugged his jacket on. "Fine, but you're telling Alec that this was all your idea."

-o.0.o-

The coffee shop seemed too crowded for an evening. All of them were mundane as far as Jonathan could tell. Most of them had turned to face a stage in the corner, no one was on it yet and he was a little afraid of what tonight's act would be.

Jace had led them to an unoccupied table in the corner so they could watch the room. "You drink that stuff black?" Jace nodded towards the mug in front of Clary. She had been the only one who decided to order coffee.

"What's the point if it's half creamer?" She took a sip and looked over her shoulder at the door as she set her mug back down. Jonathan was starting to get a little worried about Clary's friend. Since they sat down she seemed to be getting increasingly more agitated. He wanted to dismiss it as nerves but he was paranoid that she really didn't want to see this guy.

Jonathan debated on whether or not it would be a good idea to go back to Clary's apartment after this. He leaned over to whisper to Jace, "On a scale of that time Max started a fire during his lessons to the time that Alec's bow broke in the middle of a hunt how bad is Clary's apartment?"

"To you and me, probably Max starting the fire," He smiled fondly at the memory. Somehow Max had turned into a mini Jace in the last couple of years, much to Hodge's displeasure. Jonathan pitied him for having to deal with two Jaces in a row. "To Clary probably the equivalent of the demon at Pandemonium saying your father's name."

Jonathan blew out a sigh just as Clary turned back to face them. The look on her face told him she had heard the exchange. "You want to go back to my house?"

"Clary!" The three of their heads snapped in the direction of the voice. An awkward looking boy with glasses was making their way towards them.

Clary hopped up and met him halfway. "Simon! I've never been so happy to see you, you won't believe everything that's happened in the last few days." She pulled him into an embrace that he let linger a little longer than necessary. Jonathan peeked over at Jace to see if he was imagining things. His face was calm but his jaw was set. Jonathan couldn't tell if it was jealousy that Clary was paying attention to someone besides him or if he already decided he didn't like the mundie. It was probably both.

"There must have been a lot going on if you wouldn't text me back," Simon replied as he released Clary. His eyes moved from her unwillingly to check out the table where Jonathan and Jace sat. "Clary, who are your friends?"

Jonathan looked from Clary's anxious face to the coffee mugged she abandoned and wished for a completely different type of drink. "Does Hodge still keep a bottle of scotch in his desk?" Jonathan muttered to Jace.

"Not since Alec found it after his last fight with Robert," Jace was thoughtful for a moment, "Drunk Alec wasn't as fun as I hoped."

"Uh, Simon—I mean um," Clary stammered through her explanation. Jonathan wanted to help her but thought better of it. "Jace, Jonathan, this is my best friend Simon," She gestured between the three boys as a way to introduce them, "Simon, this is Jace and Jon—my older brother."


	6. Chapter 6

**Author's Note: Assume any time I update this fast, I'm supposed to be doing something else. Please review :)**

 **Disclaimer: I do not own TMI/Shadowhunters or the characters.**

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Jonathan wasn't entirely sure how long Simon stood staring at him without speaking but it was long enough that Jonathan started to feel uncomfortable. He looked away from the blank look on Simon's face and turned towards Clary, "This might be a conversation we should have in _private_ ," he suggested.

"Right," Jace agreed, "Clary, it might be easier to explain back at your apartment." What they both meant is that they would be surrounded by proof and Simon's reaction would be contained.

"Clary," Simon said slowly, turning his body to face her. Clary did everything in her power not to look at him, "You don't have a brother." He said it like he was correcting her on a history fact. _No Clary, George Washington was the first president of the United States._

Jonathan and Jace stood up to join them. "Yeah, I was shocked too," Jonathan adjusted the collar of his jacket to keep his runes hidden from view. "But you get used to it—probably we're still working on things."

Clary held her hands out to stop the guys from moving towards the door. "Simon, do you remember those guys I saw at Pandemonium? The ones with the crazy tattoos that I said killed a guy? Remember I called you from Luke's house?"

Simon's face lit up with recognition but it immediately faded to concern. "You mean the guys that weren't there? Clary are you okay?" Jace elbowed Jonathan and when he got his attention, pointed to the rune on his neck. Unlike Jonathan, Jace didn't try to cover up his runes. He preferred to keep the mundanes from asking question through sheer intimidation alone. Simon should have noticed the "crazy" tattoo on his neck.

"Well, we're right here," Jace said in an attempt to move things along, "If you want further proof we can go to Clary's apartment and show you."

Clary looked like she was going to be sick. Jonathan hooked an arm around her shoulders for support. Simon shot the two of them a confused look. "Remember Clary you said you wanted to look for that _thing_ you lost before we went back to the insti—house," Jonathan tried to make it sound as harmless as possible to Simon even though Clary did just remind him that they had technically killed someone.

Simon grabbed Clary's arm and tugged her away from Jonathan. "Clary what are you doing alone with these people?" The only reason Jonathan wasn't irritated was because Simon seemed legitimately concerned about Clary's safety. "You were so freaked out on the phone that night. Does your mom know where you are? Does she know you have an older brother that kills people?"

Simon's voice was starting to raise and Clary looked around frantically. "Simon, not here. I'll explain everything back at my apartment. Just trust me."

Simon stepped back and gestured for them to lead the way. Jonathan hung back as Jace and Clary weaved through the tables towards the door. "For the record," Jonathan said before Simon could move, "Our mom thinks I'm dead. But let's keep that a secret between you and me." He patted the younger boy roughly on the shoulder—satisfied with the wide eyed look he received—and pushed his way towards the door.

-o.0.o-

It was hard to tell who was more hesitant to go into the apartment: Clary or Jonathan. Jonathan needed to check out the scene, he knew that, but he really didn't want to go inside. Whatever disaster waited on the other side of the door wouldn't cover up the life Clary shared with their mother, the life Jonathan would never get to have. Just the hallway outside made him feel suffocated by domesticity. As much as he wondered about what it would have been like with his mother, the safety he had grown up with inside the institute seemed preferable to the pathetic lock mundanes thought were adequate protection.

Jace stayed by Clary's side all the way up to the door. She hesitated with the key in one hand and the doorknob in the other. Opening that door would mean all of this was real. Her mother's lies were real. Jonathan and Jace were real. Demons were real. Her world was falling apart and the second she opened that door it would be official.

Jace wrapped an arm around her in support causing Simon to clear his throat loudly in response. Jace ignored him and whispered something to Clary. "Doesn't that bother you?" Jonathan had been keeping to himself a little ways away from the rest of the group. He hadn't expect Simon to try and talk to him. The only reason Simon seemed interested in talking to him was to get him to keep Jace under control and away from Clary. "Doesn't it bother you that your friend his hitting on your sister?"

Jonathan fixed him with the same blank stare Simon had used at the coffee shop. "I've known her for three days, I don't have the right to be bothered. Also, I've known her for three days and know she can handle herself. How long have the two of you been friends? Twelve years? Shouldn't you know that by now?" He wasn't going to feed Simon's obvious jealousy towards Jace. Whatever feelings Simon had towards Clary, friendly or otherwise, Jonathan would let Clary deal with them.

Jonathan decided to ignore whatever reaction Simon would have to his comments and focused one Clary. She had been able to put the key in the lock but she didn't look close to turning it. Whatever encouragements Jace was trying to give her weren't working. "Clary," Jonathan said slowly. She looked at him over Jace's shoulder with wide eyes, "We're here with you. You're safe." He'd never tried to reassure someone in this type of situation before, he just hoped he was doing it right.

"Why wouldn't she be safe? It's her own house." Simon looked between the shadowhunters and Clary for an answer.

Clary sighed and turned the key in the lock. "There's a lot we have to talk about." She pushed the door open until it hit something on the other side. It was just enough room that they could squeeze in.

Jace's reports had been an understatement. Jonathan was expecting overturned furniture and a few pictures knocked off the walls, maybe a broken window. There was all of that plus holes in the walls, splintered door frames, a couple doors knocked off their hinges—one broken clean in half—singed tears in the sofa. "Holy shit," Simon muttered from the doorway.

Jonathan and Jace spread out to search the apartment before Clary and Simon stepped into what Jonathan assumed was the main living area. Clary wrapped her arms around herself like she was trying to protect herself. Simon put his arm around her shoulders in support as he looked around the room. Jonathan prayed he wouldn't notice the blood stains on the carpet near their feet. According to Jace's report that had been where Clary was attacked.

Jace kicked through rubble in a bedroom and peeked into the bathroom. Jonathan examined pieces of broken picture frames on the floor near the kitchen. No matter where they looked, even in all the chaos around them, there was a notable absence of one thing. Blood. Aside from the stain by Clary and Simon the place was clean.

"Is this what it looked like when you came home?" Jonathan asked loud enough for Clary to hear him. When she didn't say anything Jonathan looked over to see her nod. Clary would have told him if most of this was from her demon attack, which meant most of this had been because of Jocelyn. There was too much damage for her to have done it on her own. Jonathan felt a little guilty about letting himself think Jocelyn would have left Clary too. "When Jocelyn left she was alive," He said affirmatively.

Clary pulled away from Simon and stepped over a stray couch cushion. "Really? You're sure?" The hope in Clary's voice was almost painful. Jonathan looked back down at the frames. He had said she was alive when she left, not that she still was. Clary would put the pieces together on her own later.

Jonathan pointed to the stain on the carpet. Simon looked down and jumped back with an audible noise of disgust. "That black stuff that looks a little like cigarette burns is ichor—demon blood. The red stuff is your blood. Everywhere else is clean. All this destruction and no blood? She put up a fight but they didn't hurt her, well they didn't break skin at least."

"Clary?" Attention turned to Simon. His hair was messed up from where he ran his hand through it. "What the hell is going on?"

Jace reappeared in the kitchen, walking right over a fractured door to stand by Jonathan. "The world is not what it seems monsters are all real blah, blah, blah." He waved that part off with a dismissive hand before gesturing between him and Jonathan. "We're shadowhunters, we protect you mundies from those monsters."

" _Mundanes_ ," Jonathan stressed the word as a warning to Jace. They didn't have time for Jace's petty insults especially since the person they were aimed at wouldn't understand them, "Are humans. We're—"

"We're humans? As in you're not?" Simon turned to Clary and held onto her arm. "Clary what is he talking about? He's admitting to not being human and you think he's your brother?"

Jonathan cleared his throat in impatience. He wondered briefly what would happen if he took two doses in a day. He never did before but maybe it would help calm him down and make these situations easier. Maybe it would just knock him out. "I was about to say that we're part human and part angel, it's why we can protect normal humans from the things out there. We can see them, you can't. And don't try and deny our resemblance. We both have our mother's eyes." Jonathan flashed him a smile that wasn't meant to be friendly at all and Jace tried to muffle a laugh.

Clary tried to pull Simon's attention back to her. "Jon is my brother. My parents were shadowhunters too—I'm a shadowhunter Simon." She said the last four words as slowly as she could in the hopes that would make them easier to understand.

Simon looked down at her with wide eyes. "Clary, your dad is dead. He was a soldier," Jonathan scoffed at that, Simon ignored him, "And died in a car wreck before you were born. Your mom is and artist. Remember? She has that one buyer that buys everything. We think he's secretly in love with her. Remember, Clary?"

"It wasn't a car wreck," Jace volunteered.

Jonathan shot him a look but continued with the breakdown of Simon's information, "Also crazy anarchist cult leader works better than 'soldier'," Clary gave him a confused look, "That's something we probably should have told you about before we left." Clary didn't know about Valentine or the Circle. Jonathan looked to Jace for a way to handle this but Jace decided turning a shard of glass to dust with the heel of his boot was more interesting.

Jace paused half way through his destruction and bent down to pick up a shard from one of the larger frames. "Why don't we show him how runes work?" Jace held the glass like a weapon. "Maybe he'll believe us if we show him."

Jonathan looked from Jace to the glass and back again. "I swear on the angel if you cut me with that I will kill you," His voice was even but with a light edge to it. Jace would know he was only half kidding.

Jace rolled his eyes just as his phone started ringing in his pocket. He pulled it out and gave it one look. "Izzy," He handed Jonathan the glass, "Do the demonstration while I go handle this."

Jace disappeared back into the bedroom. Simon watched Jonathan warily as he pulled his stele from his pocket. "What demonstration—," He was cut off as Jonathan tightened his grip on the glass causing it to cut into his skin, he dropped it to the floor once enough damage had been done. Jonathan held out his palm like a magician doing a trick. He hiked the sleeve of his jacket up to reveal a couple more runes and drew an iratze in a blank space at his wrist. He pushed his hand almost in Simon's face so he could watch the gashes heal themselves. "Holy shit."

"Holy blood," Jonathan corrected, "The angel blood allows us to use angelic runes to give us demon fighting abilities, like accelerated healing. Comes in handy." He wiped the blood of his hands onto his dark t-shirt in a place that the jacket would cover it. "Mine usually take a little longer to kick in," He added as an almost silent after thought. The demon blood made the runes lose a little of their effects. For worse injuries the iratzes take twice as long as they would on a normal shadowhunter, speed runes gave him just enough he could keep up with the others, and stamina runes only went so far.

He looked down at the bloody piece of glass. It had landed on the back of a picture frame. He bent down and picked the frame up, turning it over carefully as he did so. A younger Clary standing on the front steps of the building stared up at him. Her red curls had been tamed into pigtails and she had a too large backpack on. Jocelyn knelt down beside her with one arm wrapped around her. They were both laughing.

"First day of kindergarten," Clary explained without even having to see the picture. Jonathan looked up at her, not fully understanding the significance of the occasion she mentioned. "I recognized the frame."

Jonathan popped it open and took the photo out and handed it to her. "You won't be coming back here. If you can find anything else you want to take you can. Might make your room at the institute look a little more like home." She took the photo with shaking hands. "Who took it?" He asked before he could stop himself.

"My mom's friend Luke. He helped raise me. I tried to go to his house the night I was attacked but he wasn't home." Jonathan nodded and took it as an acceptable answer. He tried not to get jealous of Clary getting two parents while he had none.

"Hey Jon," Jace called, "Come in here for a second."

Jonathan stepped carefully over the broken door and into the wrecked bedroom. "Izzy get in contact with Magnus Bane?"

Jace was leaning over a nightstand, riffling through something. "Yeah, she got an invitation to his party tonight. Look at this." Jonathan heard a snap and Jace turned with a box in his hands.

It reminded him of the box the Silent Brothers put his medication in. Heavy wood with a carving on the top. Instead of the Silent Brothers symbol it was his initials. J.C. was carved in ornate letters on the lid. Mourning runes bordered the edge. Jonathan gave Jace a quick glance but his face was blank and his eyes were on the box.

Jonathan flipped the lid open and sat on the bed in shock. Baby shoes. A rattle. A lock of fine white hair. And a photo of a sleeping infant. He slammed the lid shut seconds after he took inventory. He stared passed Jace and at the wall. "Well she's in for a surprise when she gets back isn't she?" It was a lame attempt at a joke but all he felt was numbness. Jocelyn thought he was dead. Of course she did, he knew that, she left him to die. She knew what Valentine would do to him if she left. He never thought that she would regret it.

"Jon?" Clary entered the room with Simon at her heels. She had filled a small backpack with things she wanted to take with her. "Hey where did you get that?"

Jace spoke up for him. "I found it in the nightstand. You said you didn't know about him but that was right there this whole time." It was half accusation half curiosity.

Her voice was sort of dazed sounding when she spoke again, "I found it when I was a kid, she took it from me and said it was my father's. She told me his name was Jonathan Clarke." She sat down on the bed next to Jonathan, this time conscious of his need for space. She reached over and opened the box. "So that's why she told me to never touch it."

Jonathan reached behind her and opened her back pack. He made room for the box and zipped it back up. He didn't know why he wanted it. "Let's go, we have a party to get ready for and we still have to convince Alec to let us go."

"What party? Go where?" Simon demanded. "What's in the box?"

"Yeah what party?" Clary asked.

"Magnus Bane's. Izzy pulled through," Jace explained, "If we play our cards right we should be able to get that block off you."

"We're," Jonathan gestured to himself, Jace, and Clary, "Going back to the institute, it's where we live. As for the box, that's my business not yours."

Clary stood up and moved herself so she was in between the shadowhunters and her friend. "Simon is coming too so be nice to him."

Jonathan stood up too, crossing his arms to match his sister's posture. "No he is not. Mundanes are only allowed in the institute under extreme circumstances. We're pushing it even telling him about this stuff."

"I'd say these circumstances are pretty extreme," Clary countered, "According to you our father was a crazy anarchist cult leader wouldn't the Clave want to talk to his daughter no one knew about?" There was a thinly veiled threat in her question. If Simon didn't go with them, she wouldn't follow.

He wanted to tell her that breaking the law was a lot riskier for him than it was for Jace and the Lightwood siblings. His demon blood and parents stacked the deck against him. The Clave just needed one good solid reason to lock him up for good. A bunch of small infractions might land him a cell as well just maybe for a shorter time. But that wasn't fair to her. She wasn't responsible for him, it was the other way around.

Jonathan sighed and looked over Clary's head to Simon. "You get in the way one time and I will kick you out myself." He walked past both of them, ramming his shoulder into Simon's on his way to the front door.


	7. Chapter 7

**Author's Note: I apologize for this chapter being unedited but I really wanted to post this tonight and I have an early morning ahead of me. This is a filler chapter. I've decided to make Jonathan asexual because I feel like it works really well with how I've written him so far. I hope you guys like it. Please review :)**

 **Disclaimer: I do not own TMI/Shadowhunters or the characters.**

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The elevator doors were barely open before Alec got started scolding them. "No one had any idea where you were. You took _Valentine Morgenstern's_ daughter out of the institute. I was about to call Mom and Dad in Idris when Izzy stopped me. Do you know what would have happened if I made that call? There would be Clave representatives all over this place searching for her," Alec's anger was aimed mostly at Jace as they unloaded into the hallway but he turned on Jonathan towards the end of his rant, "And _you_. What were you thinking? We have reasons to believe your father has been alive this whole time, the last thing you should be doing is going places without telling anyone. Do you have any idea how bad that looks?"

Jonathan refused to acknowledge the possibility of the Clave connecting him to his father. Jace was the first to interrupt. "Hey, she's back in one piece, isn't she? Jon wanted to see Clary's apartment and I thought Clary could use some of her own clothes."

Jonathan leaned his back against the wall and watched as the argument continued. Alec listed off more rules that Jace broke by letting Clary leave while Jace continued to not care. It took Alec a while to notice Simon, who had decided hiding behind Clary from the tall, angry shadowhunter was the best plan of action. "What is that?" Alec asked when he finally noticed.

"That," Jonathan's head was starting to spin, so he leaned his head back and shut his eyes, "Is a Simon."

A hand rested on Jonathan's shoulder. "Jon, are you okay?" Clary's clear voice sounded too loud to his ears. "You look really pale, like paler than you did earlier."

He had to work hard to force his eyes open. "Damn it Jon, now you're skipping your injections too?" Alec accused, "Losing that much control is dangerous for you right now."

Jonathan tried to remember if he had taken his injection today. Between watching Clary, Clary waking up, his break down, the note from Brother Zachariah, and the coffee house and apartment it had slipped his mind. He knew he thought about taking it but he never actually went to do it. He knew Alec was right, if he started acting like the monster his father created they would jump to conclusions and claim Valentine had something to do with it. That didn't mean he was going to give Alec the satisfaction. Even if he did feel a little like throwing up. "You're in charge of the institute, not me."

"Try that on the Clave and see what they do to you," Alec shot back.

Jonathan pushed himself off the wall and closer to Alec. "You know if someone took a drink every time you mentioned the Clave they'd be dead within the hour," He said and left Jace to come up with an excuse for their actions.

He made it halfway to his room when black spots started to appear behind his eyes. Sometimes with withdrawl just made him dizzy, other times it made him black out completely. When he came to he was an entirely different person, a person that he hated with every fiber of his being. He reached out for a table and leaned on it, making the vase of flowers on it rattle. "Jon?" He blinked hard until he could see Isabelle standing in front of him. "Well I was going to ask if you were alright but your eyes are changing color."

"I had other priorities," Jonathan said by way of explanation.

Isabelle looped an arm around his waist and took on the weight he couldn't hold up. She led him down the hall towards his room. "So, I'm guessing being a big brother isn't as easy as Alec makes it look?"

Jonathan opened his door and she helped him inside. "Can you get me the box on my dresser? The one on the left." He sat down on the edge of the bed as Isabelle retrieved his medicine. "It would probably easier if Clary had any reason to look up to me. You grew up with Alec, you trust him. Clary and I don't have that."

Isabelle set the box next to him and sat down on the other side of it. It was similar to the way he and Clary had sat earlier. This conversation was a lot less awkward. "My advice is to try and keep your bitterness about your mother to yourself." Jonathan rolled his eyes, he already figured that one out. He flipped the lid open and loaded a syringe.

"I gave her two questions that she could ask and I would be as truthful as possible," Jonathan admitted. He tightened a rubber band around his arm, "You might not want to watch this." Isabelle turned her head has he gave himself his medication. There had been a time when he winced at the pinch, now it barely hurt. The bluish outline of his veins on his skin turned a dull grey as the medicine spread. "You're good."

"Has she asked anything yet?"

"She started with three, she tried to ask why Jocelyn hid all of this," He gestured with his hand to indicate the entirety of the shadow world, "And I refused to tell her because I want Jocelyn to be the one to tell her about me and my father. So she asked me about my medicine and I told her about the whole demon blood thing." He packed the box back up and laid back on his bed.

"She took it pretty well," he added as an afterthought.

He could feel his pulse in his fingertips.

Isabelle drummed her manicured nails on the top of his medicine box. "That has to count for something right? She didn't freak out when you told her."

Jonathan had always admired Isabelle's gift for being positive. It was a gift she was generous enough to share. She kept Alec from tearing his own hair out, Jace from getting into unnecessary fights, and Jonathan from hating himself. They'd all probably go insane without her.

Isabelle had always been easy for Jonathan to talk to. She had a special way of balancing empathy with logic that made it nearly impossible to feel judged by her. She didn't pretend to understand the problems Jonathan had that stemmed from his demon blood but didn't shy away from offering advice to the best of her abilities.

The queasiness in his stomach subsided. Goose bumps started to rise on his skin and he shivered.

Jonathan sighed and crossed his arms behind his head. "It's just that I know most of our conversations are going to revolve around Jocelyn and helping Jocelyn and everything we do will be a step towards getting Jocelyn back and then what do I do? Act excited to see her?"

"Of course not," Isabelle said almost immediately. Jonathan felt the weight of Isabelle and the box leave the bed. Her heels clicked across the floor to the dresser. "That wouldn't be honest. I don't think you'll know how to react until the time comes. It's not something you can prepare for, Jon."

He knew it was true but it didn't make him like her conclusion. She must have taken his silence as an end to the conversation because her heels clicked against the floor again. "I'm picking out what you're wearing to Magnus's party," Jonathan had gotten used to Isabelle's obsession with clothing over the years and learned to dodge her comments about the plainness of his own wardrobe. She did give him credit for at least having more variety than Alec. He wondered if Clary shared a similar interest. "Do you have anything besides that stupid jacket that you can hide a weapon in?"

Jonathan didn't answer because his stupid jacket suddenly felt way too warm. He kept his eyes closed while he sat up and struggled to get it off fast enough. The ten or so minutes after he took his medication were never fun but he'd take it over being irrationally angry all the time.

"I don't know," He huffed, finally responding to Isabelle.

Jonathan tossed his jacket onto the floor and curled up on his side as the effects started to fade away. "What the hell? You have this badass motorcycle jacket just hanging in here and I haven't seen you wear it once."

He couldn't think of what jacket she was talking about so he looked over his shoulder at the wardrobe she was digging through. She had tossed the jacket onto the bed next to a pair of dark jeans. He remembered it was a Christmas gift from "Santa" the year before. He had appreciated Robert and Maryse for even including him in their holidays. The older he got the more he felt like his relationship with the Lightwood parents was more professional than personal and it was a nice reminder that they didn't think of him as a total burden.

"Yeah, your parents got it for me for Christmas," Jonathan rubbed his eyes with the heels of his hands. "I really like it. It just doesn't have much of a collar to cover up the runes on my neck and I can't wear it on patrol because the leather is too thin."

Isabelle picked out a shirt and tossed it with the other clothes, "You, my friend, need to start exploring the mundane night life. Neck tattoos are actually pretty common then."

Jonathan sat up and reached for the shirt. "No thanks, I'd rather go on patrol." He pulled his grey t-shirt off and replaced it with the white v-neck Isabelle had picked out.

"Come on, I need someone to go out with other wise Alec won't let me go," She whined and crossed her arms over her chest. Her lips slid into a pout that was probably supposed to convince him but only succeeded in making him laugh. "Would it seriously kill you guys to do something besides work?"

"You're delusional if you think any of us would go to one of those places for pleasure. Jace doesn't drink, Alec's too uptight, and I'm claustrophobic. Why do you think I always offer to keep watch? I get to stay _out_ of the crowds then." Jonathan used his fingers to comb through his hair and get it to lie flat again. "And you're absolutely insane if you think having me as your bodyguard would make Alec okay with you going to a nightclub. Can you check my eyes?"

Isabelle leaned across the bed and grabbed his chin. Their faces were only a couple inches apart, most guys would have killed to be in Jonathan's position. Isabelle Lightwoods was just as gorgeous as she was intimidating. There had been a time when Alec went out of his way to keep Jonathan and Isabelle as far apart as possible to prevent a relationship from forming. Jonathan was too amused to tell him he didn't find Isabelle attractive.

Jonathan had never understood why Jace and Isabelle spent so much time on dating and sex. He didn't understand the appeal. He didn't know if it was from his excessive issues with intimacy or something else. For a while Isabelle had started bothering him about his sexuality the same way she bothered her brother about his. She had given up faster with Jonathan which led him to believe she had found out something about Alec's. Whatever it was, Jonathan didn't want to know. It was Alec's cross to bear until he decided to let them in on it.

"Green as grass," Isabelle reported and gave him a light smack on the back of his head. "Now finish getting ready. I have to go get Alec to calm down. Then, I'm going to collect your sister and play personal stylist. See ya in an hour."

Jonathan had finished changing his clothes and in an attempt to entertain himself had decided to try and straighten out the covers on his bed. It didn't really matter to him, he'd be asleep in it again soon anyway. Jace was the neat freak that made his bed within five minutes of waking up in the morning.

Someone started knocking on his door while he was in the middle of rearranging pillows. "Door's unlocked," He called while he adjusted the comforter on top one last time.

"Are you feeling better?" Jonathan looked up to see Clary standing in the doorway. She rubbed her arm awkwardly and looked at anything that wasn't her brother.

"Fine. Are you okay?" He blamed whatever lecture Alec had dished out on her. "I guess I should have warned you about Alec like I did with the Silent Brother's, huh? His sister Isabelle just left to handle him and find you. I promise she's a lot nicer."

She shook her head before he was even done talking. "No, Alec was right. We should have told someone where we were going. I was just thinking about something Jace said at the apartment." Jonathan was slightly relieved that Alec hadn't scared Clary and a little happy he had gotten through to her. Alec setting up limits for her would make things easier for Jonathan later.

"Is this something that you'd like to use one of your last two questions on?" Clary nodded and shut the door behind her. The action made Jonathan more nervous than it should have. "So?"

Clary didn't hesitate but she didn't look up from Jonathan's shoes. "How did our father die? Jace said it wasn't a car wreck and considering all of the new lethal stuff I've found out about in the last twelve hours the possibilities seem infinite."

Jonathan bit down on his tongue until he tasted blood. There really wasn't a gentle way to describe _how_ somebody died. There were thousands of different ways to say that they died: passed away, left this earth, went to a better place, etc. He knew that he needed to keep things gentle for Clary's sake but he wanted nothing more than to let it be as brutal as their father had been. "House fire. Arson," He finally said after he decided "he burned to death just like he's burning in hell" was too harsh.

"And you were in the house too," Clary said it slowly like she was testing the fact as she said it.

"How did you know that?"

"You said something about someone finding you when you told me about what he did to you," She finally looked up and when she spoke her voice was quiet and terrified. "Did you-did you set it? Did you start the fire?"

Jonathan couldn't hold back his surprise. "What?" He almost shouted, "No! I was two years old. He set it! He was trying to-," He cut himself off before he could finish, but Clary had caught it and her eyes were wide and expectant. Jonathan sighed before she could ask and in a small broken voice explained, "I told you the blood made me more aggressive but you don't know how much. I was violent, Clary, even as a toddler. He was _afraid_ of me, Clary. Valentine Morgenstern was afraid of me. He set the fire because he wanted to kill me."


	8. Chapter 8

**Author's note: So this chapter is really really long and I'm sorry I tried to cut it down some. Please review! :)**

 **Disclaimer: I do not own TMI/Shadowhunters or the characters.**

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Jonathan had no idea how Isabelle kept Alec from complaining about violating protocol. It didn't stop him from making general remarks about how bad of an idea this was, but it was nice to have a break from Jace was giving Clary a crash course in downworld etiquette behind him. Jonathan didn't really think it was necessary because he wouldn't be letting her out of his sight, if any stray vamps came a little too close he'd probably get a little too close to breaking the accords. Jonathan walked in the center of the pack with Simon and was considering entering the Lightwoods' arguments to get away from Simon's commentary on Jonathan and Clary's situation.

"It's just kind of insane that you guys grew up half an hour from each other and never knew about each other. Are you sure you didn't have _any_ idea?" It was the first time Simon had paused in five minutes.

"I was two when Jocelyn left," Jonathan glared at Simon out of the corner of his eye but the mundane boy was too concentrated on his own thoughts to notice, "And it's been twenty years. You know what memories I have of being two? None." He prayed Simon would let it go.

"Why did Jocelyn just say that Clary had a brother that died in the car accident too? Why just your dad? How did he actually die—?" This was _not_ a conversation he was going to have twice in one day.

Jonathan stopped in his tracks and turned back towards Clary. "Clarissa I swear on the angel I am thirty seconds away from strangling your mundie. _Control him,"_ He ground out through his teeth.

Jace stepped up before Clary could intervene and clapped his hand on Jonathan's shoulder. "Hey Jon, I forgot to tell you something Brother Zachariah told me before he left," Jonathan detected the cover up but Clary just ignored it and went to chastise Simon for being nosey. Jonathan and Jace fell back from the rest of the group. "Look, I don't like the mundane either but he's important to your sister for some reason. He's just curious don't let him get to you." Jace gave him a light backhanded slap on the arm. "You've worked too hard to prove everyone wrong to let some mundane make you lose control."

Jace had never been rude or mean to Jonathan but he had also never been so blatantly supportive of him or of anyone. Jonathan stared at him for a long moment before deciding on the reasons behind it. "If you want to date my sister go for it, just stop being overly nice. It's creeping me out." Jace tried to look offended but Jonathan dismissed it. "Seriously, stop it. I don't have any right to control Clary's relationships just like you don't have any right to control Izzy's. Now make a smart remark about something so we can move past this."

Jace broke out into a grin. "Oh Jonathan, all my remarks are smart. It's a sign of my intelligence."

Jonathan shook his head and laughed. "I guess arrogant works just as well."

Isabelle stopped in front of converted warehouse. "We have arrived," She made a dramatic hand gesture towards the door.

"Do you guys have an idea what he looks like? What if we can't find him in the crowd?" Alec's last minute attempts to derail the plan were weak enough that Jonathan was able to have an answer to both. Usually he felt like he didn't have a leg to stand on when Alec used logic and common sense. For most shadowhunter instinct and the need to prove themselves over powered both. Alec had been blessed with a strong sense of both and the others had been cursed to live with it.

"Spikey hair. Yellow cat eyes. Lots of glitter." Jonathan thought about the pictures they had on file of Magnus Bane. There was no way anyone could overlook him. "Trust me. If you see him, you'll know. It doesn't really matter because we won't have to go and find him. Do you really think he wants some shadowhunters at his party frightening his guests? If he doesn't try and kick us out in our first ten minutes inside I'll do _all_ of your reports for a month."

Alec gave him a look that was somehow surprised, impressed, and annoyed all at once. "And how do you know all that?"

"He looked it up on one of the computers in the basement," Isabelle had taken out a compact mirror and began checking her lipstick. "By the way the next time you step foot in my lab without permission you'll learn whips aren't always for fun." She snapped the mirror shut and looked at Jonathan with a face so sweet it had to be covering up a threat.

"Can we just go already?" Clary begged. She rubbed her bare arms against the fall chill. Isabelle had insisted on changing Clary into a sleeveless dress for the party. "It's cold out here and I want some answers."

Their group piled into the tight staircase behind Isabelle as she followed the noise to Magnus Bane's door. She paused outside the door to readjust the top of her dress and grinned. "I've wanted to go to a Magnus Bane party for years." She pulled the invitation out of her bag and opened the door without knocking. Jonathan doubted anyone would be upset that some guests were letting themselves in. They would probably object once they realized the new guests were shadowhunters.

Jonathan ducked discreetly behind Alec at the back of the group. He only had a few inches on Jonathan but it would be enough to hide him and still allow him to see everything. His face would cause more problems than the runes curling up their necks. His father and the Circle had made a stop in New York once upon a time. No one would want to go to a party with Valentine Morgenstern's son on the guest list. If they wanted Magnus's help, it would be best if they didn't destroy his reputation at the same time.

As expected, feet stopped in their tracks and eyes lingered on the cluster of shadowhunters and their mundane friend. "Well you guys really know how to make an entrance," Simon grumbled under his breath.

"They're looking at you too," Jonathan hissed back as their group moved further into the room, "At least a third of them are thinking about sinking their teeth into your neck."

Isabelle reached for Simon's arm and tugged him towards her side. "They better not," She smiled sweetly up at Simon and for a moment Jonathan felt a little bad for him. Simon let out a flustered laugh at Isabelle's sudden attention.

"I don't remember giving any invitations to Nephilim," The shadowhunters' attention turned towards a tall warlock making his way through the crowd. Jonathan recognized his spikey hair, flashy clothes, and gold cat eyes. Magnus Bane stopped a couple feet away from Jace.

Isabelle handed Jace the invitation. "Would you like to verify its authenticity?" Jace held it out at arms' length. His voice seemed genuine but the smirk on his face destroyed the illusion.

Magnus gave him a tight lipped smile back and took the invitation without looking down. The paper burst into blue flames and Jace yanked his hand back abruptly in shock. His elbow landed a blow just under Alec's ribcage. His gasp drew Magnus's attention and the tight smile eased. "I suppose as long as you promise not to murder of any of my guests you can stay for a drink or two. But fair warning, I _will_ be watching for any sign of trouble."

Clary stepped forward out of their group before Jonathan could grab her arm and keep her back. Jace should have been the one to introduce their true intentions, it would have been tense but it would have been at least somewhat professional. If he had learned one thing about his sister it was that she was assertive, a quality he both admired and hated. The second she stepped out of place his stress levels sky rocketed. Magnus's face when he noticed her was almost worth it.

Magnus's cat eyes were wide and blue sparks flickered on his fingertips as Clary stopped at Jace's side. "Clary," He murmured. His eyes darted between the rest of them and landed on what little he could see of Jonathan. "Pretty boy, take a step to your left," Jonathan wasn't sure who he was addressing but Jace stepped aside without hesitation but that only offered Magnus a better view of Simon. "Not you, _you_." He pointed at Alec.

Blood rushed to Alec's cheeks but he stepped aside without a word. Jonathan was still blocked from the view of most of the downworlders but Magnus's eyes flickered with anger and recognition. "You look just like your father," Magnus's voice had taken on a cold edge that made Jonathan want to grab Clary and leave before he could get any closer to her.

"How unfortunate for me," Jonathan shot back in a low voice.

Magnus's stare stayed on him for one long minute before he turned back to Clary, "I'm assuming the protections wore off since you've shown up with shadowhunter body guards. I'm also assuming that since you're here, you want answers."

"At this point, I really only care about my memories," Clary seemed unfazed by Magnus's hostility towards Jonathan. "As far as I'm concerned my brother and the Lightwoods can help fill me in on the rest."

Magnus laughed at Clary's confidence. "If you think that you shouldn't have even come here, Biscuit." He gestured towards one direction of the crowd. "Follow me." The group made to follow him but he held out his other hand to stop them. "Just Clary."

Jace hissed, "Not a chance."

Jonathan seemed to be the only one surprised by Jace's blatant distrust of Magnus. The way he saw it, they didn't have a choice. There could have been a time when she was younger when she heard her mother slip up and say something. There could have been something she'd seen that could help them. Maybe there had been a time when Jocelyn mentioned him. "What Jace means to say," Jonathan said pointedly, "Is that we think it would be best if the two of us went with her. She and Jace have become friends and she trusts him. It's probably an easy assumption to make that I need some answers as well."

Magnus examined the boys for a brief moment before deciding the fight wasn't worth it. "Fine. You two can come, tall dark and handsome back there can guard the door, and you keep the mundane away from my other guests—they'll tear him to pieces if he makes the wrong move." The last instruction was aimed at Isabelle. Jonathan thought briefly that splitting up like that would be a bad idea. It was either that or let Clary go alone. He didn't have any reason to distrust Magnus, his mother had trusted him to protect Clary after all, but he was worried about how Clary would take the information.

Jace was about to object to this new plan but Jonathan cut him off, "That's acceptable."

Magnus ignored Jonathan's approval and led the way towards the crowd. A hand grabbed Jonathan's shoulder and held him back. He slowed his pace and looked up at Alec. "Why don't you ever express any interest in diplomatic missions? Aside from the sarcasm at the beginning there, you did really well." As the oldest Lightwood child, Alec was set to inherit control of the institute when his parents retired. At some point, Jonathan wasn't sure when, Jace, Jonathan, and Izzy had made a silent agreement to stay in New York with him.

Jace would stay with his parabatai no matter what, even if it was in New York. He wasn't exactly fond of the city and had been pretty open about the fact since he arrived at the institute for the first time. Isabelle was exceptionally intelligent in math and sciences. There were probably ample opportunities for her in Idris, stuff like studying demon species and consulting the Silent Brothers, but she never had any desire to leave her brothers or active duty.

Jonathan would have probably been able to get a job working in Idris if he wanted. He didn't have Izzy's level of specialty in anything but he enjoyed learning languages and translators were always a good thing to have around for when shadowhunters from across the globe visited. He always knew in the back of his mind that if the Clave offered him a job it wouldn't have much to do with his qualifications and a lot to do with keeping an eye on him. Answering to Alec seemed preferable.

"I want you to find ten people—shadowhunters and downworlders—that would trust Valentine Morgenstern's son," Jonathan was about to pick up his pace again but he decided that his point wasn't as strong as he wanted, "Actually, I want you to find ten people, who don't know me, that would be willing to _talk_ to me."

Alec dismissed his concerns with an eye roll. "Look, I know that I've been saying you need to be careful with the possibility of your father being alive but the best way for you to prevent people from comparing you to him is to let them hear _your_ voice. If you don't they'll just assume it's the same as his."

Jace, Clary, and Magnus were waiting outside a door in a short hallway. "Man, I don't want to talk about this. I'm fine with going on patrol and turning in paperwork like everyone else. I don't need to prove anything." Jonathan made it a point not to look at Alec as they came to a stop. He had accepted a long time ago that anything he did would be twisted by the shadowhunters that think he should be locked up. Anything he did in an attempt to prove them wrong would be seen as a cover up for something imaginary and awful. The other three had clearly overheard the last part of their conversation but he imagined the defeated look on his face was enough to stop them from asking.

Magnus ushered Jonathan into the room after Clary and Jace and lingered in the hall for a moment to give Alec instructions. Jonathan thought it was a little strange that he felt the need to give such detailed instructions to someone who was trained to protect things but he refused to say anything.

The room they had entered was clearly Magnus's bedroom. The room wasn't messy but it was definitely filled to capacity with clothing, knick-knacks, and antiques. Jonathan was terrified of touching anything but it didn't stop Jace from picking up a small wooden figurine and inspecting it. Magnus shut the door and plucked the figurine out of Jace's hands on his way into the room.

"I can't just give you your memories back but I can pull a few threads of the spell that will make it unravel in its own time. It could be days, it could be years before you are able to remember everything significant." Magnus set the figurine down on a dresser and sat down in an armchair. "Of course you'll only regain memories that the block would have prevented from sticking. Normal everyday things that anyone would forget won't come back. Some memories you already have might start to look different. Your mother for example, I assume you don't remember the scars on her arms and legs? Her neck?"

Clary looked like that last comment had struck a nerve. Jonathan thought about the scars covering his own arms, some from injuries but most of the raised white lines on his arms were ghosts of old runes. It hadn't occurred to him that Jocelyn would be covered as well. "Simon told me about the scars," She muttered, "I thought he was crazy."

"Exactly," Magnus leaned back in his chair triumphant, "Usually the spell is strong enough to even erase the small details of the shadow world from you memory almost instantly. Over time it would start to weaken. Your mother would bring you back every couple of years so I could strengthen the spell again. You were actually due for a booster anyway. I was going to try and talk Jocelyn out of having me do it again. You'd be eighteen soon anyway and the Clave wouldn't be able to recruit you even if they did know you existed."

Clary looked to Jace and Jonathan for an explanation to that comment. "Sometimes shadowhunters leave the Clave," Jonathan explained, "Their runes are stripped and they go to live a mundane life. Shadowhunter blood is dominant so even if they marry and have children with a mundane they're still going to be shadowhunters. The Clave checks in with the children every year starting when they're about eight or nine to see if they'd like to start training. Eighteen is the cut off. Since no one knew you existed, representatives were never sent."

She nodded once to say she understood but she turned back to Magnus a second later. "Was it the Clave or Valentine she was running from? Did she know he was still alive?"

Magnus glanced over at Jace and Jonathan like he really wished they would disappear. "She _suspected_ your father was still alive. I remember when Jocelyn first came to me she was adamant that he had faked his death. Now with the rumors going around about those murders and Jocelyn's disappearance I'm inclined to believe her."

"Clary?" Jace reached out to graze his fingers against her wrist, to get her attention. She was staring at Magnus with a blank look in her eyes. The little color she had in her face was gone making her freckles more prominent.

Jonathan took a step towards he but stopped, he had no idea what to do. "He took her. I know he did." The anger made her voice shake.

Magnus stood up and walked towards her in one fluid movement. "Well you won't be any help finding her if you're still blind to half the shadow world. May I?" He held his hands out on either side of her face. She gave him the go ahead and he place his fingers against her temples. Clary squeezed her eyes shut tight as blue sparks came from Magnus's fingertips.

It was an unsettling sight to say the least. Watching the sparks seem to absorb into her skin and seeing her cringe in discomfort more than pain. When Magnus took his hands away Clary swayed on unsteady feet. Jace hooked an arm around her waist before she could fall. She kept her eyes shut but reached up to rub her forehead. This time Jonathan didn't hesitate on his way towards her. It was Magnus that grabbed his arm that kept him back. "Is she okay? Clary?" She was just barely out of arm's reach but the wince on her face made him feel like she was a lot further away.

"She'll be fine, it's just a head ache," Magnus snapped his fingers and a stack of papers appeared in his hand. He handed Jonathan the papers. "She'll be back to normal in a few minutes." The assurance did little to settle the anxiety bubbling in his stomach.

Jonathan had been curious after he found out Magnus had helped Jocelyn. He didn't understand why he would help her and his reaction to Jonathan's resemblance to his father suggested he had even more of a grudge against Valentine than most downworlders. "Um, did you ever know our father? Personally I mean."

Magnus pulled up the hem of his shirt to reveal a gruesome looking scar in his abdomen. "He stabbed me if that's what you mean." He swallowed and looked at someplace behind Jonathan's head. "I was the one who called the Whitelaws the night they were all killed. They ran the institute before the Lightwoods."

"Why did you help my mother if you knew what she married?" Jonathan demanded.

Magnus sighed, "I really need a drink," He mumbled and snapped his fingers for two glasses of whiskey to appear on the table beside them. He handed one to Jonathan. "If anyone needs alcohol it would be you." Jonathan set the glass back on the table. Zachariah had told him he wasn't allowed to drink in his condition.

"I wasn't going to help your mother, my friend Tessa Gray just happened to be visiting when Jocelyn stopped by with Clary and a dear friend of hers had been a Fairchild woman decades and decades ago so she had a soft spot. Also Clary was still just a little toddler at the time—could barely walk, only could say a few words and screech _a lot_ —and Tessa loves babies," He rolled his eyes, "She encouraged me to help them. Jocelyn and I established a sort of working relationship after that. She'd call to make sure there wasn't any word of her going around, or if she should be worried that Clary wanted to read a popular book series about vampires when she was in middle school.

"It wasn't until Clary was around ten that I realized I actually cared what happened to them," Magnus admitted, "I only saw her once every couple years but it was interesting watching someone grow up. You better take care of her."

Jonathan was a little surprised to hear the threat in Magnus's voice. "Of course I will," He didn't try to hide how offended he was, "She's the only member of my family—of the shadow world—that doesn't let my demon blood impact how she sees me. I'll help her find Jocelyn and protect her the whole way. I'm not throwing this away."

"Does my mother know?" The color had returned to Clary's face and she didn't seem to be leaning on Jace as much as before. "Does she know Jonathan is still alive? That he's been a half hour subway ride away this whole time?"

Magnus shook his head. "Jonathan's _treatments_ were still relatively classified information at the time," Jonathan shuddered at the remaining memories of the Silent Brothers' first few attempts at curing him, "Je—Zachariah wasn't allowed to speak of it when Jocelyn needed assistance. Even if she did it wouldn't have changed anything. She was convinced Valentine was still a live which means he was probably watching you at the institute. She wouldn't risk your safety when the stakes were that high."

"Wait," Jace's head snapped up, "Do you think it's possible Valentine has been watching the institute this whole time?"

"Oh, he's definitely watching Jonathan," Magnus removed all the what-ifs with that one statement. What if Valentine was alive? What if he knew Jonathan was alive? What if he's been watching them? "You were a bomb he was too scared to detonate and now you're in someone else's hands. He'd want to know if they figured out how to defuse you."

"But you knew," Clary accused. She pushed Jace away and stepped towards Magnus, "You knew he was alive but didn't tell her."

"Look, Biscuit," Magnus's tone reminded Jonathan a little bit of the way Alec would speak to Isabelle when she was annoying him. It bothered him more than he would admit that Magnus felt comfortable speaking to her that way when he was afraid to be alone with her most of the time. He tried to tell himself it was just because she still had one question left and he had no idea when she was going to use it or what she would use it on. "I would have told her if I didn't think it would upset her so much. Not only would she find out her son is alive, but he's in control. And she wouldn't be able to see him."

It was at that moment that Alec and Isabelle decided to burst into the room. Isabelle lingered behind her brother like he was going to protect her from the others. Alec took a deep breath before rushing out the news. "We have a problem. The mundie's gone."

Jonathan didn't even get a chance to process the idea that his mother might actually want him.


	9. Chapter 9

**Author's note: Look at that, I reasonably sized chapter for once. Please review :)**

 **Disclaimer: I do not own TMI/Shadowhunters or the characters.**

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"What do you mean _he's gone_?" Clary shouted. Jace grabbed her arm as if he was trying to restrain her.

Alec still had his hand on the doorknob and he looked up at the ceiling as he spoke. "Well it's a little more complicated than that. We can't find him partially because he's a rat and partially because we think the vampires might have taken him thinking he was one of their drunk friends."

Clary shook Jace off and marched towards Alec. Jonathan held his arm out to stop her and pulled her in the second she walked into it. It would be amusing watching little Clary try and take on Alec at any other time, but right now there was a possibility of laws being broken. "What do you mean _he's a rat_?"

Magnus looked at Isabelle over Alec's shoulder. "Green drink?" Jonathan saw Isabelle's dark hair nod. "That's why you shouldn't hire Seelie bartenders. If you'll excuse me I have someone to fire." He brushed against Alec's side and Alec shoved his fist in his pocket a moment later.

Alec cleared his throat to explain, "He drank something before Izzy was able to warn him and he got turned into a rat. Some vampires can turn into small rodents. They probably thought he was one of them and took him."

"Clary, I'm _so_ sorry," Isabelle tried to get around Alec so she could talk to Clary face to face but he held her back. "I tried to stop him but he already drank too much and there was nothing I could do. I tried to catch him but he was too fast. I saw one of the vamps leave with a rat and I'm not even one hundred percent sure it's Simon."

"Well we have to get him back," Clary fought against Jonathan as she spoke. "We can't just stay here! Jon, let me go or so help me!"

"I'll let you go when I can trust you not to attack anyone," He explained. "We're going to head back to the institute and figure out something there. Something tells me this party is going to break up fast once Magnus gets rid of the bartender."

"Agreed," Alec nodded once and turned and ushered Izzy out the door.

Jonathan let Clary go once they were out of sight. She turned on him the second he did. "We can't go back to the institute! We need to figure it out now!" She back handed his arm to punctuate her point. He held up his arms to keep her from lashing out at him again. "What happens if the vampires didn't take him or he got away? What if he turns back in the middle of the sewer with no idea where he is? What if he never turns back?"

"Clary," Jonathan kept his voice as even as possible.

"What if he-"

"Clary!" Her mouth snapped shut when he raised his voice. He rested his hands on her shoulders. "Clary, let us handle this. We're trained for this. The more you protest the more time we waste. Let's go."

Clary remained quiet on the way out of the building while Jace and Jonathan both tried to find a way to reassure her. Jace made a few weak attempts at humor but Clary ignored it in favor of looking pissed off. Alec and Isabelle were already well up the block. Alec had his arm wrapped around her shoulders and had his head bowed as he spoke to her. He was probably reassuring her that she had done everything she could. It wasn't until Jace mentioned Alec's name that Jonathan's brain was able to come up with anything sound.

"Damn it," Jonathan said louder than he meant to.

Clary looked up at him, startled by his sudden outburst. "What is it? Is it about Simon?"

Jonathan was hopeful about his sudden epiphany but he wasn't thrilled about what he would have to admit out loud. "Yeah. Good news is I might have a solid way to save Simon that we could act on without having to go back to the institute. Bad news is it might take some convincing to get Alec on board. Also I might have to admit he was right about something. I'll be right back."

He took off jogging towards the Lightwoods siblings. They weren't walking very fast but they had gotten a decent head start. "Alec!" Jonathan called ahead. Alec pulled Isabelle to a stop and turned to his head. Jonathan came to a halt in front of them. "I have an idea that might not just get us Simon back but might actually lay some groundwork for a possible relationship with the Dumort vampires."

Alec raised his eyebrows at Jonathan's confidence and the possible diplomatic element to whatever Jonathan had planned. "Before I say anything, you are not allowed to try and recruit me until after we get Clary's mundane back. Deal?"

"Fine, I'll just let you prove my point for me." Alec smirked and Jonathan debated if Isabelle's wrath later would be worth punching Alec now. It wasn't often that Alec looked smug—he was generally pretty modest—but when he did he could be a dick about it.

"We go right to the Hotel Dumort but we don't enter and we don't bring any weapons aside from what we already have on us. We knock on the front doors, throw something at the boarded up windows—whatever we can do to get their attention without entering the building. We request to speak with Raphael Santiago directly about a matter that concerns the Accords," Jonathan began.

Alec seemed to remember the same bit of their conversation from the day they met Clary that Jonathan had. "Raphael hates the idea of breaking the accords. How would you get him to talk to us about it?" Jonathan was relieved that he wasn't rejecting the idea yet. He had been worried that the idea of walking up to the front doors of the Hotel Dumort would be a deal breaker.

"We don't tell the Clave about tonight's incident," Alec opened his mouth to object but Jonathan held his hands up to shush him before he could speak, "And if he refuses to meet with us we tell him that if he doesn't we will give him a few days to change his mind before we are forced to call the Clave. That way he knows that as long as he cooperates we stay on a local level and he won't have any Clave reps searching his place.

"We say that we have some concerns about something that happened at the party. If he still doesn't agree we tell him the truth: that an incident may have happened that would lead his vampires to accidentally breaking the accords." Jonathan was so used to the shadowhunter way of omitting information that the idea of being able to deliver so many truths was refreshing.

Alec crossed his arms but nodded along. "Alright, play into his fear of messing with the shadowhunters, I'm listening."

"At that point he'd have to come down and talk to us. We tell him a mundane drank a fairie drink and the effects may have made it easy for the vampires to mistake him as one of their own. Then we tell him we didn't call the Clave because we figured things would turn ugly fast even though this whole thing was probably just an accident. We say we just want to do a quick search of the place—Izzy you saw what Simon looked like right?" She nodded and looked a little bit like she wanted to cry at the reminder. "We make a point to say the search won't be thorough, just a quick look at all the residents. If he agrees to call them all to the lobby we won't have to go beyond that.

"If he still doesn't want to take the chance and trust us," Jonathan shrugged, "The drink will wear off eventually and boom: Simon's a real boy again. Raphael will know we were telling the truth and deliver him immediately to the institute. We let him go because no intentional harm was done.

"Either way the vampires hand over Simon and either way we prove ourselves reasonable and trustworthy." Jonathan was a little nervous when he wrapped up. Alec's expression hadn't changed at all and he knew with Alec acting as the head of the institute this was his call.

"I'm still not a fan of the idea of not going to the Clave. Is there any way we can do this but still report to the Clave when we get back?"

Jonathan was shaking his head before Alec was done. "No. Listen to me, our biggest bargaining chip is giving them a short window of immunity. It shows we're willing to negotiate instead of just running to the Clave to clean up the mess. We'd be assigning them blame when this whole thing is just one giant accident. We need to present ourselves as understanding. If we help them get out of this we gain a little bit of their trust."

"Jon?" He looked away from Alec and towards Izzy's frantic voice. She reached out and dug her fingernails into the sleeve of his jacket. "Jace and Clary aren't behind us anymore." Jonathan spun around faster than he thought he would have been able to.

The sidewalk behind them was empty except for a few stray drunken party goers. "I'm gonna kill him," He said before he could stop himself. "If he took her where I think he took her, I'm gonna kill him."

"Hey," Alec grabbed onto his arm, "They could have just taken a short cut."

Jonathan glared back at Alec. "You've met Jace, right?" Alec took his hand back and raised both in surrender.

Isabelle searched her bag for a moment and pulled out her phone. "We'll just call him." Jonathan knew the second she dialed he'd never pick up. It only took a few seconds before she hit his voicemail. "Jace, it's Izzy. Whatever it is you're about to do, please, please don't be stupid."

"Too late," Jonathan called loud enough for the receiver to pick it up.

Alec had pulled out his own phone and was typing away at the keys. If Jace wasn't answering phone calls he definitely wasn't answering his texts. "Well that didn't ease my worries at all. The institute is that way," Alec pointed towards the direction they had been headed. That kind of seemed obvious, but Jonathan kept his mouth shut, "The Hotel Dumort is that way." He pointed towards the way Clary and Jace would have gone.

Jonathan had been angry with Jace before but at that moment panic turned his stomach upside down. "If he lets her set foot in that hotel it won't be the Accords he'll have to worry about." Jace wasn't around but Alec was the next best thing so he aimed the warning at him instead.

"Not so fun being the big brother with such an eager little sister is it?" Alec shot back.

Years ago Jace and Jonathan had undermined Alec's decision to make Isabelle stay at home instead of accompanying them on patrol. Alec had just wanted to keep Izzy safe but they couldn't justify leaving such a skilled fighter back at home.

"This isn't the same situation," Jonathan growled through his teeth, "Clary doesn't have _any_ training. She just found out she was a shadowhunter this morning. Your parabatai is about to take on an entire clan of New York vampires basically on his own and you're going to use this time to say I told you so?"

"Jace can handle himself," Isabelle offered, "I'm sure he won't let anything happen to Clary. The best we can do right now is head to the institute and change into gear. Jace will send a message if he needs back up."

"So nothing? We're going to do nothing?" Jonathan didn't mean to raise his voice and he instantly regretted it when he saw Izzy cringe.

"Isabelle is right," Alec said, "More shadowhunters showing up at the Hotel Dumort unannounced will seem like an attack. Diplomacy goes beyond saying a bunch of nice sounding words, Jon. It's also knowing when to hold back."

Jonathan grumbled a dismissal and started to head back towards the institute. His head ached and the pounding of his pulse in his ears made him feel like he had missed a dose of his medicine. If this was what having a little sister was like, no wonder Alec was so pissed off all the time.


	10. Chapter 10

**Unusually Long Author's Note: Sorry this is another chapter that gave me some trouble. I should have the next one up soon. Really fast though I want to answer a couple questions from the reviews and ask a couple of my own.**

 **\- I may include some of Clary POV later but you probably won't see Jace POV.**

 **-Jonathan's demon blood works like it did in the book with a little bit of stuff I add (ex. the runes not working as well and later on you'll find out they hurt more on his skin). He's not quite as strong as the others as a result of his medication.**

 **My questions: I have a one shot "Too Soon" that a couple people said they would like to see a continuation of it would the people who read that like an angsty story based off that? Or I was thinking about my next story being about the Chicago Institute's shadowhunters? Which would you guys rather read?**

 **Disclaimer: I do not own TMI/Shadowhunters or any of the characters.**

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By the time they walked through the institute doors Jonathan had imagined about a thousand different ways Jace and Clary's raid of the Hotel Dumort could end and most of them were horrible. By the time the three of them had gotten changed and sat back down in the conference area waiting for Jace's call he had thought of another fifty. He tried every exercise that Brother Zachariah taught him to try and keep the demon blood induced thoughts away to calm himself down.

Every now and then there would be days at a time when Jonathan's medication didn't seem to work that well. For the most part he would be able to contain the hostility towards himself, but bottling it up did little to help anything. He'd lose sleep from horrific and realistic nightmares and just about anything he ate tasted wrong. By the time the episodes would pass he'd be exhausted and a little faint.

Brother Zachariah had told him the best thing he could do was focus on the most outlandish detail and start to break it apart until he could refute it.

He started with the idea that the second they set foot in the hotel they would be swarmed. Vampires were fast but they weren't that fast. And they had trouble working together. Werewolves were in packs because teamwork was easy for them, vampires were the exact opposite. By nature vampires were gluttonous, if they weren't going to get more blood out of a situation they weren't interested.

The only reason such large groups of vampires had gotten common was because of the Accords. It was a lot easier to stay out of the eye of the Clave if they hid among others of their kind. The worst Jace and Clary would encounter is seven or eight vamps at most. It wasn't ideal but it was a lot better than the whole clan.

He worked his way through his list of worries until he was faced with the most realistic. Clary had the same reckless behavior as Jace with significantly less training to back it up. He couldn't think of any way that _wouldn't_ get Clary in trouble.

Isabelle and Alec were flipping through files on the screen. Jonathan was too focused on his task to know what they were looking at. Their lack of concern for Clary and Jace made his blood feel like it was ready to boil. Jace was Alec's parabatai, shouldn't he be more concerned? Shouldn't Isabelle be worried one of her best friends might be getting hurt right at that moment?

His stomach started to twist again and he laid his head down on the table. _Alec and Izzy aren't worried about Jace because they know he can handle himself. Jace can handle himself._ _He'll look after Clary._ Doubt began to flood his thoughts almost instantly.

"Jon?" Izzy's voice came from somewhere near him. "Are you okay?"

He stood up fast enough that his vision turned black for a moment. "I'm going to go to my room. Come get me if they call."

Izzy followed him out of the room and grabbed his arm before he could get too far. "Seriously Jon, are you okay?"

He reached up and rubbed his temples, "Look Izzy, I just really need to lie down for a while. This whole little sister thing is a lot harder than I thought it would be and I'm getting a headache. Please."

Isabelle let go of his arm and let him head off towards his room. For the second time that day he thought about what would happen if he took a second dose of his medication. His symptoms had never showed up this strong after he took a day's injection. It could have been the start of one of his slumps but he couldn't risk it with Clary's arrival.

He shut his door and stared at his room. The last time he had been in here Clary had been standing by the door asking about his father. She had gone quiet when he told her why Valentine had started the fire that night.

There wasn't really an appropriate reaction when your older brother told you that your father tried to kill him. He just told her not to worry about it which was probably the least comforting thing he could have said.

His thoughts slid back to the Hotel Dumort and Clary's lack of training. He winced at the images of blood and fangs flashing through his head. His eyes locked on the boxes on his dresser. He had a whole box full of doses, he had enough that one extra dose wouldn't be missed

Maybe it would stop the scenarios from playing out in his head and ease the tightness in his chest. He thought of Alec and Izzy, calm and rational in the control room and wondered how they could pull it off.

He didn't hesitate on the way to the dresser but paused with his hand on the latch. He was sick of being the only one out of control. How would Clary ever trust him if he couldn't figure out a way to keep himself in check?

Isabelle always looked to Alec when she was in trouble and he never hesitated to fix it for her and he never let her know what stress he was under. He should be able to do that for Clary.

Jonathan stripped off his gear jacket and opened his box of medication. His hands were steady as he loaded the syringe, to his surprise. Usually when he got to the point when he started seeing things he would be shaking and sweating.

He gave himself the injection, trying hard to predict the outcome of this decision. Admittedly, Jonathan had never been anywhere nearly as careful as Alec but he never got too close to Jace's reckless edge. This was probably the closest he had gotten to Jace's impulsiveness.

He put everything away as carefully as possible and sat on the edge of his bed and waited. The usual chill didn't come and neither did the heat wave. He just started to feel heavy, like his limbs were made of lead.

His eye lids began to slide shut and he laid down on his side. Jonathan tried to calculate how long it had been since he took his first injection of the day, but the numbers didn't make sense. He thought he had been worried about something but he couldn't quite remember what it was.

 _Clary_. Something had happened to Clary or Clary caused something to happen. _Something with Clary._ His thoughts started to blur and fade until he was completely unconscious.

-o.0.o-

Cold fingers pressed against Jonathan's neck just under his jaw. "His pulse is back to normal," Hodge's voice was low as he moved around beside Jonathan's bed. "He'll probably be awake soon. You can all go to bed, I'll stay up with him."

"If he's going to be awake soon why would we go to bed?" Clary protested quietly, "You need to check on Simon anyway. I'll stay up with him."

"He means," The authority in Alec's voice seemed out of place among the other's soft voices even if he wasn't speaking all that loud, "That we shouldn't all be in here. It's good bedside manner to let a patient readjust without a bunch of people in the room."

Alec left with a comment about needing to check on his sister. "I'm going to go get cleaned up, do you want me to bring you a change of clothes?" Jace asked. His voice was a little hoarse when he spoke. He sounded exhausted. It bothered Jonathan that he didn't know how much time had passed since he got back to the institute.

He forced his eyelids open and blinked against the dim light. Clary ignored Jace's question. "He's up," She said a little louder than she had probably meant to speak. "Jon, are you okay? What the hell were you thinking?"

He turned his head and squinted against the light on his bedside table. Hodge was watching him warily from the corner, probably checking to make sure he didn't overdo it. Jace and Clary stood side by side a few feet away, clothes torn and dirt and blood smeared on their skin.

"What the hell was _I_ thinking, the girl who ran off to a vampire hotel asks," His sarcasm probably would have been better if he had been able to put any volume or force behind it. Jonathan had no idea how long he had been out but he knew it had been long enough that he had no right to feel as drained as he did.

Jace gave Hodge a quick look. "This seems like something that should happen between siblings. I'm going to go ahead and turn in. Good night everyone."

"And I'll go check on your friend, Clary." Hodge and Jace left a little too eagerly. They had been in between enough of Alec and Isabelle's fights that they knew it was best to steer clear.

Clary waited until the door shut behind them to step forward and kneel by the bed. "Jace and I can handle ourselves, we're shadowhunters. Why did you feel the need to knock yourself unconscious?"

"First of all," Jonathan tried to sit up but it didn't quite work. Clary got up and helped prop him up on a couple pillows. He muttered a thank you and tried to ignore the aches appearing all over his body.

Clary sat down on the edge of the bed and stared at him. He had to give her credit, she had one hell of a poker face. He couldn't tell if whatever had happened with the vampires had traumatized her or affected her at all. Or just how mad at him she was for risking the second dose. It was a little intimidating.

"First of all, you literally became a shadowhunter a day ago. You didn't know anything about this until twenty—well I don't know how long ago because, as you've pointed out, I was unconscious. My point is that you shouldn't be acting like you know everything." Jonathan could feel his strength returning the more he spoke but he had a feeling it was his worry from before coming out that made him so talkative.

"Jace has training, Clarissa, he's one of the best," Jonathan explained, "But he's not exactly the most predictable in battle. You don't know anything about fighting, you would have no idea what to do fighting beside him. If I'm being honest I'm a little surprised you made it out with a few cuts and scrapes.

"I had a plan to get Simon back, one that would have been a lot less of a headache. I spent the entire way back to the institute thinking of every way that your little mission could go wrong. You couldn't even take a second to figure out one before you jumped in head first?

"Don't worry about me and what I did. I was stupid," He faintly remembered giving himself the second injection but he didn't remember his rationale for doing so, "I wasn't thinking clearly. Just do me a favor and concentrate on taking care of yourself just as much as you do everyone else?"

Clary looked down at the blankets covering Jonathan and cleared her throat. "Can I use my third question now?" Her voice sounded so small that Jonathan felt a little bad about scolding her. He had to remind himself that with their mother M.I.A. it was his job to keep her safe and sometimes that would mean chastising her.

He sighed and leaned back into his pillows as far as he could. He stared up at the ceiling and the old beams that ran across it. The light from the lamp by his bed made interesting shadows across the plaster and wood. "Why not?"

"Have you ever thought about—would you ever," She paused and took a deep breath, "Did you ever consider getting your runes stripped and becoming a mundane?"

Clary had a habit of knocking him off guard with her questions. _At least it's the last one_. He tilted his head to the side so he could see her again. She waited for her answer just like the last time. "Why would I?"

She looked down and played with the frayed hem of her dress. "I just thought it might be easier for you if you could live in a way that no one would know there was something different about you."

"Clary," Jonathan sighed and shook his head with what little strength he was gaining, "I wouldn't be living it up in some one room apartment in Brooklyn, working during the day and partying all night. I would be in one of your mundie prisons. Or locked up where ever they put the people that see things and get angry at the drop of a hat and have violent tendencies.

"The second my runes come off and I sacrifice my title as a shadowhunter I lose access to my treatment," He chose his words carefully so he wouldn't frighten her.

"I've read up on mundane medicines," he confessed, "I thought they might help take the edge of but they won't work. Mundane medications help fix chemical imbalances in the brain, Izzy explained it to me. My condition is a mutation of my DNA and not one mundane doctors have figured out."

Clary's face turned a little pink like she was embarrassed she had thought of the idea at all. Jonathan didn't want her to feel ashamed for trying to look out for him. He was actually a little surprised that she had been thinking of ways for him to get out of his situation at all.

He leaned his head back and stared at the ceiling. "Besides," He made his voice as light as possible, "If I did that I would be proving everyone who ever called me an abomination right. I'd rather see their faces when we turn our father over to the Clave. It would be a lot more entertaining for me."

He was a little surprised to hear Clary laugh at that. He was being partially serious, actually he was being a lot serious. Her laugh faded into a yawn. Jonathan looked back down at his little sister. "You've had a long day, you should go to bed," He nudged her knee with his hand. "We need to start your _actual_ training tomorrow. And not just the fun stuff like seraph blades and combat but the boring stuff like memorizing runes too."

Clary groaned and stood up. "Gee, I can't wait." Jonathan laughed at his sister's false enthusiasm as she shut the door behind her.

He moved as slowly as he could to stretch and turn the light out. The muscles in his torso ached as the witchlight went out, plunging his room into darkness. He shoved the extra pillows out of the way and let himself relax back into the bed. Training was going to be difficult tomorrow.


	11. Chapter 11

**Author's Note: I'm sorry, I lied. This chapter ended up being harder to write than I thought. Please review. :)**

 **Disclaimer: I do not own TMI/Shadowhunters or the characters.**

* * *

Getting out of bed was the worst plan Jonathan thought he ever had and then he tried stretching out before training. He groaned as he reached his arm out touch his toes. The ache shooting through his muscles made him want to give up and curl up on the floor.

"That bad, huh?" Clary kicked the heel of his boot gently.

He straightened up and tried his best to hide his wince as his muscles protested. "I feel like I just went three rounds with a greater demon—which probably means nothing to you, just know I'm in a lot of pain."

"That's what you get for doing something so stupid," Clary crossed her arms over her chest and looked down at him with a disapproving expression.

Jonathan stood up and brushed his hands off on his t-shirt. "I fail to see how taking a medication for symptoms I was experiencing is dumber than walking into a vampire infested hotel without any training." Clary opened her mouth to respond but shut it when Jonathan gave her a look that dared her to question him. "That's what I thought. Now stretch out, I'm going to go set up some mats. If Jace comes in here trying to distract you tell him to go away, he's probably hiding from Alec anyway."

Clary sat down on the floor where Jonathan had been and he went to drag a couple training mats out into the middle of the floor. "Okay what is with Jace and Alec? I can't tell if they get along or not. Jace said something about Alec last night that made it seem like he looked up to Alec and then he goes and does a bunch of stuff Alec doesn't approve of. I don't get it."

The soreness in Jonathan's shoulders was getting easier to ignore the more he moved around. The mat hit the floor with a satisfying thud. "They're parabatai. It's kind of like having a best friend and fighting partner but like a thousand times more intense than that. They have to go through this whole ritual thing that basically binds their souls together. They feel when the other is hurt or dying and all that."

Clary reached out to touch her toes like Jonathan had but came up a couple inches short. Jonathan laughed at her failed attempt. "So does that make Izzy your parabatai?"

Jonathan pulled another mat out and pushed it against the other with his feet. "No," He shook his head as he tried to straighten the mats out, "That's not how it works. You don't _have to_ have a parabatai. They're just nice to have. Runes applied by your parabatai work better, last longer, you fight better at their side, that kind of thing. Most people pick someone they're training with because the ceremony can't be performed if they're over eighteen."

"If you're going to commit to something like that wouldn't you have to get along better than Jace and Alec do?"

Jonathan was shaking his head before she finished. "Some parabatai have a relationship where they think of each other as the greatest warrior to ever live and all the gushy stuff and then there are parabatai like Jace and Alec who for all intents and purposes are brothers. They fight. They make up. They joke around. They'd kill for each other.

"You just got here at the wrong time. Usually Alec isn't so stressed—not that he's my favorite person when he's not—he's just been put in charge of the institute and kind of a high profile investigation at the same time. Investigations aren't like normal patrol, there's a lot of hoops you have to jump through. Patrol you just got out and walk around on some rooftops and check out some alleys. Investigations you have to file mission reports, get them approved, gather evidence, create a whole casefile." Jonathan was starting to bore himself trying to explain protocol.

"Basically it's a lot for Alec to handle. Jace was actually pretty helpful since there wasn't much wiggle room for him to go and do whatever he wanted. Then you showed up at Pandemonium and I heard the address you gave the cabdriver and suddenly there's a lot more interesting things for him to be doing. Jace running around on his own is just another thing Alec needs to keep track of. And then he brought you back to the institute and we realized you were my sister that no one knew about and things got even more complicated."

"Let me guess," Clary stood up and started stretching her arms out over her head, "That's why everyone is so eager to start my training? Because I can't cause trouble trapped in here with you."

Jonathan grabbed two of the training swords from a rack on the wall. "No—well, yes—but it's mostly for my piece of mind. You need to learn to defend yourself at least a little," He held out one of the swords to Clary and she took it warily. She gave it a small, hesitant swing. "No offense for now, defense is more important for you. You just need to stay alive long enough for one of us to get to you."

"I don't want to have to be a burden if I don't have to," The two of them stepped on the mat and positioned themselves opposite each other. "I don't want to just defend myself until someone can come and rescue me."

"As admirable as that is—feet shoulders' width apart—offensive techniques take more time to learn. Defense is just a matter of holding the sword up the right way. Offense takes more thought than that and hell of a lot more strength than that." Clary followed Jonathan's instruction with an eye roll. "Less dominant foot forward that way when you step forward your shifting your dominant side forward."

"Isn't the best defense a good offense?" She asked instead of taking the half a step forward.

Jonathan tilted his head back and groaned. _This. This is why Alec hated training with Izzy when they were younger_. "Okay fine, show me what you got." If he couldn't convince her verbally he'd just have to show her.

"Really?" Her surprise only made him more sure his plan would work.

He smirked and readied himself. "Show me what you got, Red."

Clary made the most predictable strike imaginable, straight for the sword itself and not for Jonathan. He parried the attack easily, even with the soreness in his muscles. Clary let out a disgruntled sound and took a shot for his side. He blocked it again. She brought the sword straight down, aiming for his shoulder. He ducked out of the way and pushed back so fiercely she dropped her weapon.

"Now you don't have a weapon and Jace is free to decapitate you or shove a seraph blade through your heart, depends on how dramatic he's feeling that day, and save me," Jonathan bent down and grabbed her sword and held it out to her. "So defensive strategy then?"

Clary scowled and took the sword. "You cheated," She grumbled, "That last move seemed a little offensive to me."

Jonathan shrugged her complaints off, "Sometimes pushing the weapon away can cause your opponent to lose it."

"Well, I didn't want to hurt you. You're my brother," Clary explained, "If you were a demon I'd be trying harder."

"And I'm sure if you were training with Jace or Izzy you wouldn't go hard on them because they're your friends. Or if it was Alec it would because you don't want him to not like you," Jonathan continued with her logic, "You think I'd let you do anything out there that you're too scared to do in here? No way. We're all shadowhunters, we can take it. We've been beating the crap out of each other for years. Don't be afraid of hurting us."

Clary rolled her eyes, "Fine. How do I block?"

Jonathan was relieved that his strategy had worked. "Get into the stance from before," She followed his orders, "First, if someone brings the sword down vertically like you did there at the end, stepping aside isn't always necessary. Just hold your sword out horizontally. Here," He held onto her wrist as he moved her arm into the right angle.

"And don't hold on that tight, you'll lose feeling in your fingers in a couple minutes," Jonathan advised upon seeing Clary's white knuckles around the hilt of the sword. "Common mistake. Solid grip doesn't mean tight grip."

Clary nodded and readjusted her fingers. "This doesn't seem like it would be that effective. Wouldn't the tip of their sword still be able to graze me?"

Jonathan stepped back and got ready to demonstrate. "Not if you have the angle right," He did a slow motion version of the strike and stopped when he hit Clary's sword. His weapon stayed several inches away from her. "See? It depends on your attacker's height but you'll find your instinct is your most useful tool when you're estimating that kind of thing."

"What if I don't have that kind of instinct?" Clary let her arm drop a little. "What if my instinct tells me to keep it just a little lower than I should and I end up with stitches in my head?"

"Shadowhunters rarely use stitches, healing runes take care of cuts and scrapes pretty easily. It doesn't matter because you're a shadowhunter, you have those instincts." Jonathan reset his position, a silent signal for Clary to do the same.

"Now this I when you would get a little offensive, as you put it. If I was actually attacking you I wouldn't be going so slow. Speed and strength go together. The faster my sword is moving the harder you're going to have to push back to stop the strike." Clary nodded to show her understanding.

Jonathan laid his sword against Clary's like he had already finished the strike. "What's that supposed to do?" Clary looked at the swords than up at Jonathan. He had to stop himself from laughing. She looked a little bit like the youngest Lightwood, Max, during his training. Wide-eyed and confused when their trainer doesn't explain right away. Max as too little to even get into swords yet, he was still doing basic hand to hand combat training.

"I'm going to start pushing down, your job is to keep me from moving your guard down. That way you have an idea of the force you'll have to match. Okay?" Clary nodded and squared her shoulders.

Jonathan started push against Clary's block. She hesitated at first but began pushing back before he would have been able to cause real damage to her defense. "Like this?" She asked as he started pushing harder. Clary's arm didn't move an inch.

"Exactly," Jonathan smiled to himself. She was actually listening to him and taking his advice, "Now remember it's not going to be gradual like this. It's going to be abrupt. Again that's probably going to be an instinct thing to match their force. If you're not positive with how much force you need, _always_ go with too much."

Clary glared up at him, "That sounds like offense."

"It sounds like covering your bases," Jonathan shot back. "Pull it off and you might be able to get them to lose a little ground. Want to try?"

"Bring it, Blondie," She mocked.

Jonathan stepped back into position. "If you're this cocky already I don't think I want you spending any more time with Jace," he muttered. He brought his sword down slower than he normally would but closer to what Clary might encounter in battle and she blocked it with ease. "Now this time push it away. I'm left handed so it's going to be easier for you since you're right handed, the angle is less awkward that way. Just push me to that side," He pointed to his left and her right, "That gets me even further away from you and— _if_ you have the right training—opens up my chest and stomach for you to take a shot at. Ready?"

Clary nodded once. Jonathan preformed the same move a little faster than before. Clary deflected it perfectly, pushing his arm and sword to the side. What Jonathan hadn't expected was for Clary to drop _her_ sword, grab his shoulder, pull him down, and knee him in the stomach hard enough that he dropped to his knees and struggled to get his breath back.

Jonathan grasped at his stomach and looked up at a smug Clary. "What the hell was that?" He gasped.

"Offense," She said simply. When Jonathan continued to stare up at her in shock she took pity on him and explained, "Mom and Luke made me take self-defense lessons, they said it was because I was a young woman in New York but I'm starting to think they had other motivations behind forcing me to take them. They were kind of fun though."

Clary shrugged and she held out her hand to help Jonathan stand up. He had to stay slightly hunched over due to the stabbing pain in his abdomen. "Way to prove me wrong, but never—and I mean _never_ —drop your weapon like that," He warned, "There's no guarantee you'll get it back. As for this Luke guy, you mentioned him before right?"

"Yeah, I think I said something about him at the apartment. Why?"

"Do you think he might know something about Jocelyn? About any of this?"

Clary looked at the wall behind Jonathan's head and shook her head. "I don't know. I think—maybe," She paused and squeezed her eyes shut, "I think I remember something. Not something Magnus took from me, at least I don't think it is. Before I went to Pandemonium I heard Luke say something about going to see Magnus. It didn't seem that important, I figured he was some art gallery owner that wanted to display some of Mom's work. I ignored it."

Jonathan didn't take long to process the information. That sliver of information was enough to confirm there was someone else out there that might be able to get them information. "I think we're going to have to talk to Luke. Alec won't be thrilled but we don't have to tell him. He was a friend of Jocelyn's right? It's probably something you and I could do this afternoon."

"Wouldn't not telling Alec upset him?" Clary asked.

"Lots of things upset Alec, I don't have the time or the patience to not do all of them. Change into your mundane clothes. If Luke helped Jocelyn keep this from you he probably won't be thrilled with you showing up in gear. He definitely won't be thrilled to see me all runed up next to," Jonathan advised.


	12. Chapter 12

**Author's Note: Here is a very long chapter that I didn't proof read because it's one a.m. and I just finished watching Vampire Academy and the main menu music has been playing for ten minutes while I finished writing this and it's starting to get a little annoying but I wanted to publish before I went to sleep. Please review :)**

 **Disclaimer: I do not own TMI/Shadowhunters or the characters.**

* * *

Luke's house turned out to only be a short train ride away. Jonathan and Clary were standing on his front stoop within the hour. "Does it look like he's home?" The front blinds were closed and the thin windows on either side of the door were covered in a layer of grime just thick enough that nothing in the dark foyer was visible.

Jonathan took a step back and looked up and down the street for witnesses. They weren't going to break in if they didn't have to. An opening rune would probably do the trick but Jonathan didn't like the idea of using his stele in broad daylight. Without glamour he felt like any mundane passing on the street was staring at him.

He was suddenly extremely aware of the runes curling their way across his skin. Jonathan adjusted his jacket collar in an attempt to hide the blocking rune wrapping around his throat.

"I don't know," Clary said honestly, "I have my key, but I'm not entirely sure I want to go inside."

Jonathan looked down at his sister and saw the thinly veiled fear on her face. He knocked his elbow into hers gently to get her attention and opened up his jacket. "I've got a seraph blade. If there's anything in there, I can take care of it."

Clary shook her head. "That's not what I'm worried about. Luke wasn't here the other night and when I got back to my place it was wrecked. What if Valentine got to him too?" She stared at the door lock like it was about to come to life.

"Then there might be something inside that can help us," Jonathan reminded her. "Here. Turn around, hold your hair up."

She looked up at him in surprise. "Why?"

Jonathan reached into his jeans pocket and pulled out his stele. "Courage in combat rune. It's the best I can do for right now. The first time you get a rune it usually looks a little gruesome and now's not the time for you to find out what that looks like. Turn around." Clary did as she asked and Jonathan gave the street one last look before angling himself to block the rune from sight as he drew it at the base of his sister's neck.

The second the stele touched Clary's neck she flinched away. "Does it always burn like that?"

Jonathan debated on whether or not he should answer. For most shadowhunters the burn of a stele was painful, but something they'd get used to after a few years of using it. He remembered watching Alec wince as he applied soundless runes to his forearms and then almost overnight Alec stopped showing any signs of the pain.

He understood Clary's pain. The demon blood came with a lot of side effects, mostly behavioral but some were physical like his dark eyes and the paleness of his skin and hair. It also made his body try and reject the runes. They were angelic in nature and the demon blood made it hard for his skin to take the and sometimes that meant they were more painful.

He finally settled on, "It's different for everyone. You'll probably get used to it eventually. There. All done."

Clary let her hair fall back over the red symbol burned into the back of her neck. "That was unpleasant," she muttered and started fishing around in her pockets for her keys, "I still don't want to go in. I think your magic wand thing is defective."

"Well you're not in combat yet so the courage is dormant. Hope you don't need it." Jonathan pocketed his stele. "And it's called a stele. Looks like you're going to need vocabulary lessons too."

Clary unlocked the door and shoved her shoulder against the door, "It sticks," She said by way of explanation, "And sorry if we have culture clashes. You grew up with steles and glowing swords; I grew up with paint brushes and pepper spray."

Jonathan followed Clary into the dark house. He couldn't help himself, "They're called seraph blades, Clarissa." She turned to glare at him but he refused to wipe the smile off his face.

"Dear god, how does Isabelle deal with Alec?" She grumbled as she led the way through a small living room filled of mismatched furniture. It was more cozy than crowded. The space was domestic and comfortable, not the disaster zone Clary's apartment had been.

"Consider yourself lucky," Jonathan said absently as he inspected the coffee table. There was a paper on the table from four days ago and a stack of mail and more recent papers on the corner like someone had set them there sometime today, "Izzy's got three brothers. Two older, one younger. In all honesty Jace is probably more annoying than Alec."

Clary tiptoed towards into a hallway. From where Jonathan stood he could see the doorway that led to the kitchen. "Jace said that he'd been living with the Lightwoods for ten years, haven't you been living with them since you were a little kid? Do they not consider you a son too?"

Jonathan and reached down to flip through the envelopes. Mostly bills, a few pieces of junk mail. "Uh no, the Maryse and Robert think of me more as a responsibility. Robert was Jace's godfather which means when Jace's father was killed the Lightwoods adopted him. Technically, I'm just a stray shadowhunter living at their institute."

It wasn't until after the words left his mouth that he realized he wasn't painting the Lightwoods in the best light. "They treat me fairly well, don't get me wrong. It's just that most of our time growing up I wasn't exactly stable. I wasn't exactly a safe training partner for their kids. Jace was trying to get Alec to be his parabatai when I was allowed to start training with them."

That got Clary's attention. She turned her back on the hallway to look at him. "You spent most of your time growing up in the same building as them and you never spent time with them?"

"No," Jonathan shook his head, "I wasn't allowed to _train_ with them. I still sat in classes with them and had dinner with them and that stuff. My condition just makes me a lot stronger and faster—part of the reason our dear old dad put me through this—and if I lost control I could have seriously hurt them."

She seemed to be comforted by his answer and turned to walk into the kitchen. Jonathan followed her this time. There didn't seem to be anything extremely out of the ordinary in the living room as far as he could tell, and Clary didn't seem particularly concerned about the state of it.

Jonathan stepped into the hallway and half a second later a large dark figure lunged at him, taking him to the ground. It twisted his arm behind his back at a painful angle and put their knee in his lower back. His other hand was crushed beneath his chest from where he tried to break his fall.

"Luke!" Clary exclaimed, "What are you doing?"

Luke's weight pressed Jonathan into the floor. The handle of the seraph blade in his pocket lodged itself in his ribs, and the zipper of his jacket angled itself in a way that it bit at the skin of his stomach through his t-shirt.

"Do you have any weapons?" Luke demanded of him.

"Just a dagger," Jonathan gasped out, "Inside jacket pocket."

"Is it silver?"

"No, it's a seraph blade. All adamas. I swear."

Luke let up on his pin just enough to reach under Jonathan and search for the dagger. He found it after a couple seconds of searching and tossed it out of Jonathan's reach.

"Luke," Clary begged, "Let him up. That's all he brought."

Jonathan was grateful to have the seraph blade out of his ribs. He tried to use Luke's newly loosened grip to try and get into a slightly more comfortable position. Fighting back would only make things worse and he definitely did not have the upper hand. He succeeded in shifting in a way that his knuckles weren't pressing against his chest.

"Clary, you wouldn't be saying that if you knew who this really is," Luke sounded like a worried father trying to reassure his child. It took Jonathan a second to remember that _was_ Luke and Clary's relationship. He blamed it on his restraints being more than a little distracting.

"I know who he is," Clary assured him, "Jonathan Morgenstern. My older brother. You and Mom think he's dead but he's not."

Jonathan stared at the woodgrain in the floor and waited for someone to say something that would get him off the floor.

"Clary, you don't know about your father," Luke sounded sympathetic, "What he did to him."

"You mean how my father is apparently some murderous crazy guy that fed my mom demon blood when she was pregnant because he wanted to turn my brother into some super shadowhunter or something and then when that backfired tried to kill him?" Jonathan had to admit Clary summarized the situation pretty well. "Yeah, I know about it. Now let him up. He's not dangerous."

"If you don't believe her, look at my eyes," Jonathan volunteered, "Jocelyn probably told you about them, right? How the blood turned them black?"

"He has Mom's eyes, Luke," Clary said softly.

Luke's grip slacked a little more and Jonathan's arm was able to relax a little. "It could be a glamour."

"Actually it's a medication," Jonathan corrected, "The Clave had the Silent Brothers make it for me. Can I _please_ sit up now?"

Luke let go of Jonathan and stood up, "Sit up but stay on the ground," He ordered.

The soreness from this morning had been almost gone when Jonathan and Clary got to Luke's house, but the impact and the angle Luke had held his arm at had made some of it flare back up. "See, green as grass," Jonathan opened his eyes wide and looked up at Luke. He was fully aware of how foolish he probably looked, but this wasn't exactly a fun situation to be in and his irritation at getting pinned to the floor wasn't helping. The sooner he could get it over with the better.

Luke stared down at him in shock. "You look just like your father," He mumbled.

Jonathan rubbed his shoulder. "Why does everyone keep saying that to me? You know it's not a compliment right?"

"Do you believe me now?" Clary demanded. "I don't know why you won't since I haven't spent the last eighteen years lying through my teeth."

Jonathan couldn't help but feel a little proud of his sister standing up for herself. "Clary," Luke's voice held a warning, "We were trying to protect you."

Jonathan watched Clary carefully. Her green eyes looked a little too shiny. "Clary?" He asked quietly.

"Your _protection_ worked out so well since Valentine got my mom," She snapped, "Were you just never going to tell me about all of this?"

Luke pressed the heel of his hands to his eyes and groaned. "We were. I tried to get your mom to tell you about most of this but she kept pushing it back. We were going to tell you two years ago but she knew if you were sixteen you'd still be able to leave her and join the Clave if she did. She panicked. And it wasn't exactly my place to tell you."

Clary faltered. "Is that why you wanted to go see Magnus? To convince her I should have my memories back?"

Luke looked surprised. "You know Magnus?"

Jonathan was starting to think they forgot about him sitting on the floor. "He's the one who told us about his arrangement with Jocelyn. A Silent Brother found the block on her memory and pointed us in his direction."

That got the two of them to look back down at him. Luke swallowed and his gaze flickered back up to Clary. "You've been busy," It was an attempt to sidetrack her and all of them knew it.

It did not, however, get Jonathan any closer to being allowed to stand up. Luke still didn't trust him enough for that. Jonathan squeezed his eyes shut and took a deep breath. "She also snuck away and broke into the Hotel Dumort to get back her mundane friend," He blurted.

"You did not just _tell on me_ ," Clary snapped at him.

"It's called full honesty, Clarissa," Jonathan looked up at her, only slightly apologetic, "Something that is seriously lacking in this room."

"Clary is that true?" Luke cast a disapproving look down at Clary. "Do you have any idea how dangerous that was?"

Clary held her hand up to stop him, "I already got the lecture from Jon, I don't need it again. Now Magnus only knew so much and I really need ans-"

At that moment someone started banging against the front door, successfully ending the conversation. "Graymark! We know you're in there!"

Luke looked frantically around the hallway and kitchen. "The two of you need to get upstairs. Now. Get your dagger and go."

Jonathan snatched up his seraph blade and jumped to his feet. "Mind telling me who your visitors are?"

"Not anyone you want seeing either of you. The last thing any of us need is for your father to know the two of you are going around the city on your own."

Clary grabbed Jonathan's arm and dragged him towards a narrow back staircase. There were several doors in the hallway, Clary pulled him into one at the front of the house. "Watch the floorboard by the closest, it squeaks really bad," She advised as she shut the door quietly behind them.

Jonathan heeded the warning and took a path towards the window facing the street that let him stay as far away from the dresser as possible. There were two men in dark clothing, too nice to be gear but it was somehow looked distinctly shadowhunter-ish, standing on Luke's stoop.

He couldn't see, but he suspected Luke had opened the door. The men's posture shifted slightly like they were talking to someone. "Does this window open?" Jonathan whispered, tapping the pane with his fingernail.

"Yeah, but it's loud if you do it too fast," Clary moved to stand next to him and looked down at the window. "They work for our father? Why do they want Luke? Why did they call him by that name?"

"Graymark is a shadowhunter name. I'm guessing that's how he met Jocelyn, they were in the Circle together," Jonathan said. "My guess is they either suspect he has information on your where-a-bouts or they don't like the idea of a downworlder knowing Circle secrets."

Clary looked up at him, her eyebrows furrowed. "Luke is a downworlder?"

"Werewolf," He answered simply until he saw that she still seemed confused, "When I told him about the dagger he asked if it was silver. Silver burns werewolves. He was being cautious," He explained.

Jonathan pulled his stele out of his pocket and pushed up the sleeve of his jacket. "Open the window, you'll probably do it quieter than I would," He ordered. He pressed his finger to his lips to tell her to be quiet as she started to pushing the window open.

The stele burned a hearing and sight rune into his skin. He had been smart to tell Clary to keep quiet because as soon as she was done with the window she pointed to the new marks on his skin. He tapped one with his finger and pointed to his ear and tapped the other and pointed up at his eye. She seemed to understand.

Jonathan ducked his head to listen through the open half of the window. One of the men moved just enough that he could see a red circular rune on his neck. He looked up at Clary and pointe to his face and mouthed _Dad_ , hoping she would understand. This time it took her a couple of seconds but she nodded that she understood.

He focused on the conversation. The rune made it sound like they were having a conversation in the room Jonathan and Clary were currently in. He probably could have heard without it but he didn't want to risk missing something important.

"Lucian, we know it's not a coincidence that you and Jocelyn _both_ came to New York," One of them said, "You have to know something about Valentine's daughter."

"I thought Valentine and Jocelyn had a son not daughter," Luke said, playing the ignorance card. Jonathan could have told him it wasn't a wise move.

"They did. She was pregnant with their daughter when the two of you ran off together," The other man snapped.

"I helped Jocelyn get out of Idris," Luke said, "I took her to an airport in France and we went our separate ways."

Jonathan wondered if that was true, if Luke really hadn't known where their mother went when she fled. And why did she chose New York? Cities would be good for hiding. Everyone was anonymous in a city.

"Then what brought you to New York if it wasn't Jocelyn? She probably came here for Jonathan," Hearing the man say his name sent chills down Jonathan's spine.

 _Act shocked. Pretend you don't know I'm alive._ Magnus had told them that Jocelyn didn't know he was alive, it would be best for Luke to pretend he still believed that too. "Jonathan's still alive? Valentine didn't kill him?"

"Why would he try and destroy the greatest weapon he's ever created?" Jonathan felt sick to his stomach. If Valentine valued him so much he wouldn't have tried to burn him alive.

Luke scoffed, "If Jonathan is a weapon why is he having you looking for Clary?"

Jonathan felt every muscle in his body freeze. Clary must have even been able to hear as well because her face paled. "Huh," One of the men said, "You claimed you didn't even know Jocelyn had a daughter yet you have a nickname for her."

 _We're screwed._ Jonathan grabbed Clary's arm and pulled her away from the window. "We need to get out of here," He whispered. He pulled her along behind him and led her towards the back of the house. They ducked into one of the back rooms, probably Luke's. The other room had a bed but it was made, this one had been slept in.

Jonathan went to the window and pushed it open. Clary helped him take the screen off the window and set it by the wall. "We aren't seriously going to go out the window," Clary said as Jonathan leaned out the window and looked out at the small yard in the back. It seemed like it was mostly weeds but there were bits of a broken concrete patio below them. It wasn't ideal but it would have to do.

"I'm not risking taking you down the stairs and out the back door. The sooner I can get you out of here the better." He stuck one leg through the window and straddled the frame, awkwardly hunched over in the small space. "I'll drop down first, I've had that kind of training. When I'm ready, you jump and I'll catch you, okay?"

"Uh…" Clary took a slight step back.

"Clary," Jonathan put as much force behind her name as he could, "Do you trust me?" She barely nodded but it was enough. It had to be enough. "Then you should know that I can and I _will_ catch you."

Jonathan swung his other leg over and tried his best to keep his balance in the cramped frame long enough for him to prepare himself for the drop. It really wasn't that high, not for a shadowhunter. The training room at the institute had beams up towards the ceiling—much higher than this-that were built specifically for learning to jump from heights. The drop was probably intimidating to Clary.

He pushed off the ledge and prepared himself for the impact. His feet hit the ground with a thud, nothing the traffic outside wouldn't cover up. He didn't even lose his balance.

Jonathan turned around and looked up at the window. Clary's bright red head was sticking out the window. She seemed uncertain, but Jonathan silently begged her with a gesture for her to jump.

Her head went back in and her legs swung out. Jonathan readied his arms as she took one last look over her shoulder. She closed her eyes and pushed off.

Jonathan took a single step forward and caught her easily. The impact sent a shock back up through his arms and he suddenly remembered every ache and pain from this morning. He stood her back up on her feet before she even reopened her eyes.

"Oh my god," Clary muttered as she looked around the yard, "I just jumped out of a window."

"So when it's your life on the line the, you hesitate to do the reckless thing but if it's someone else's life you're all for it. I can respect that," Jonathan noted.

She looked up at him with wide eyes, "You _actually_ caught me."

"Of course I did," He pretended to be insulted, "I just found out I had a little sister, I haven't decided if you're annoying enough that I want to get rid of you yet."

Clary glared at him but he ruffled her hair. Jonathan didn't even think about doing it, it was just a reflex, something he had seen Alec do to Isabelle for years. "Come on, we have to get out of here," Clary rolled her eyes and led him towards a gap in the fence.

They stepped into an alley. "That way," Jonathan pointed to the left and they both took off running. No one stopped them which meant the two men from the Circle were the only ones that had showed up to talk to Luke. They must have thought he either wouldn't be home or wouldn't be difficult to take down if they found him.

They had made it to the subway before Clary started to panic. "What are they going to do to Luke?"

Jonathan thought about all the horror stories about his father that he had heard over the years. He never understood why people had thought it was appropriate to remind him of such despicable things when they were so terrified that he would turn out the same way. For now, he decided, it was best to keep it all to himself. "I don't know," he lied, "That was quite a slip up he made."

Clary watched as a train came into the tunnel and started to slow. "Jon," she said quietly, "No offense, but I really wish it was still last week and I was just worried about scheduling classes."

As much as Jonathan enjoyed having anything close to a family connection, he wished for that too. He wanted to go back to last week too, when he only had to worry about keeping random mundanes alive. It was a hell of a lot harder looking after one specific person.

"The only thing going back to last week would accomplish is making you go through all of this again," He said quietly.

"But I could have decided to go with Mom and Luke to Luke's country house for my birthday instead of insisting we stay in the city so I could go to some stupid night club. I could have—"

Jonathan cut her off by grabbing her arms and turning her to look at him. "Clarissa, listen to me," He sounded more frantic than was probably comforting but he had to get her to listen, "Valentine is a sick, twisted man. He's also a man that was capable of tracking our mother down when the rest of the shadow world believed her to be dead. There is _nothing_ you could have done to prevent this. It would have happened no matter what. You deciding to go to Pandemonium was probably the best thing you could have done, do you understand me? If we hadn't crossed paths, if I hadn't told Jace how to find you, we wouldn't know for sure the Valentine was back. We got a demon to tell us that information but that means _nothing_ in the eyes of the Clave. You've given us a very valuable lead, Clary. If it weren't for you it would take a lot longer to find you and our mother."

Clary looked up at him with large, round green eyes. She looked like a little kid and for a second Jonathan felt very young himself, a little boy who didn't know what to say but knew something had to be said, " _This is in no way your fault,"_ He stressed every word hoping it would sink in.

In a movement so sudden it startled Jonathan, Clary wrapped her arms around his neck and buried her face in his shoulder. He wasn't quite sure what to do for a moment, but he returned the hug hesitantly. Such strong displays of affection weren't something he was completely used to. "You're a good brother," She muttered just loud enough for him to hear her, "Even if you do tell on me."


	13. Chapter 13

**Author's Note: Sorry it took so long I wasn't sure where I was going with this for a while.**

* * *

Jonathan knew he should probably fill out a report about their close call with the Circle members, but he wasn't positive if Alec had even told the Clave about Valentine and the Circle in the first place.

He had a lot of time to think about it on the way back to the institute. Once their train had pulled in Clary had gone silent for the rest of the trip. His thoughts had shifted between plotting their next plan of action and the fact Clary had called him a good brother.

The compliment didn't feel incredibly accurate when he couldn't think of anything he could do to say to her. Jonathan hoped that coming up with a next step would help him think of something to say but he was coming up with nothing. Anything he came up with required getting closer to their father than he wanted to risk.

Valentine was officially looking for both of them. Every second they spent out of the institute was a safety risk.

It took approximately four steps into the control room for the two of them to be ambushed by Jace and the Lightwoods.

"What the hell, Jonathan?" Alec asked as he came to a stop in front of them. Jace and Isabelle stood on either side of him, closing in the circle, "You were flipping out last night after Jace took Clary to the Dumort and now you're running after her without telling anyone where you're going?"

"We went to see Jocelyn's friend Luke, we were looking for information," Jonathan said in their defense, "That's a little different from raiding a hotel full of vampires with one and a half shadowhunters. There wasn't any reason for us to tell you, it wasn't supposed to be dangerous."

"I'm not half a shadowhunter," Clary protested.

"She's right," Alec said without looking down at Clary, "She's more like a quarter. Either way you should have told me or Hodge before you left the institute. You're not really in the position to be making calls like that after your stunt last night, Jonathan."

Jonathan had to admit that lately his stress had been getting to him but he didn't think that was worth treating him like he was a child. He opened his mouth to tell Alec this but Jace jumped in before he could make a sound, "You said 'it wasn't _supposed_ to be dangerous', which means something happened."

Alec and Isabelle looked at Jonathan expectantly. "Shortly after we arrived two Circle members showed up to confront Luke about what he knew about Jocelyn and Clary. Then they started talking about me too, how Valentine wouldn't want me dead because I'm a weapon or something which I think means since he couldn't kill me I might as well be useful somehow. Luke made the mistake of asking something about why Valentine was looking for Clary if he wanted me."

"And, let me guess, no one had said Clary's name until that point?" Isabelle guessed.

"Exactly," Jonathan confirmed, "I got us out of there immediately. We don't know what happened to Luke. I was more worried about getting Clary to some place safe."

"That _is_ a good question," Alec said as he crossed his arms over his chest, "If Valentine didn't know about Clary why would he be looking for her? She's not part of his plan, at least not his original plan. And he's known where you've been for years apparently, he had ample time to take you away. Besides, your medication makes you too docile. It's basically a sedative. You're not exactly weapon material most of the time."

Jonathan had thought about what had brought his mother to New York, it turned out he should have been wondering what had brought his father here. "What if he was just looking for Jocelyn?" He suggested, "Wanted her back or something."

Clary shivered next to him, "Can we please not phrase it like that?"

"I doubt he'd risk his cover just to get the wife that left him back," Isabelle said, "Maybe she just had something he wanted. Something she took from him when she left."

Alec stepped back and started to pull something up on the nearest monitor before she was done talking. "Clary, you're eighteen right?"

"Yeah, my birthday was the day I ran into you guys at Pandemonium," She answered as the rest of them moved to huddle around Alec.

"It was a yes or no question," He muttered as he pulled up a case file, "This is the report from the fire and these are the reports filed about the Uprising." The screen split itself to accommodate both files.

A photograph of Fairchild manor burning was at the top next to large red letters that spelled out "Case Reopened." Jonathan's stomach turned as he read through the basic statistics. Under the category of "survivor" his father's name had joined his. Under the category of "deceased" his grandparents' names had been joined by John and Baby Doe.

The other file was an overview of damage done by the Circle during the signing of the accords in the nineties. The dead were in three separate lists, Circle members, shadowhunters loyal to the Clave, downworlders.

"Valentine set that fire a couple days after the Uprising. Aside from Jocelyn and Luke there was one other thing missing after," Alec said tapping his fingers against the screen to pull up a picture as he spoke. The Mortal Cup filled the screen. "I'm not saying this is why Valentine came back but if a Circle member snatched the Mortal Cup for him or if he took it himself during the chaos of the fighting going on, wouldn't he have used it by now?"

"What is the Immortal Cup?" Clary asked.

" _Mortal_ cup," Isabelle corrected, "It's one of the holy objects of the shadowhunters. Mortal cup, Mortal Sword, Mortal Mirror. The cup allows us to create shadowhunters out of mundanes, but the turn out rate isn't great. Most mundanes die during the process."

"Also anyone in possession of it can control demons," Jonathan concluded, "Which would probably be why our father would want it. Why make new shadowhunters when you can get the ones already here to bow down to you?"

"So you think our mom stole some sort of magic cup from Valentine and he wants it back?" Clary clarified. "Why didn't Luke say anything?"

Jace shrugged, "She might not have told him she had it."

"Or it could have been that most of the time we were at his house he had me pinned to the floor," Jonathan offered, "That can be distracting."

Isabelle and Jace both gave him quizzical looks but Jonathan dismissed them with a wave of his hand. "Okay," Jace said slowly, turning his attention back to the task at hand, "The way I see it we have two options: we find something we could track Luke with or we wait and see if Clary's memories start coming back and she remembers seeing the cup someplace."

"I could go back to Luke's and get a shirt of his or something," Jonathan volunteered, "It's probably better that Clary stays here now that we know for sure our father is looking for her."

"He's looking for you too," Jace pointed out, "I've been to Luke's before I can go and get something. You can stay here out of sight."

"Actually," Isabelle interjected, "It would probably be a better strategy to keep Jon and Clary separate. If we keep them in one place Valentine only has one place to keep eyes on and strike, separate them and Valentine will be forced to divide his forces."

"Wait, why does anyone need to go get something from Luke's house?" Clary demanded. She really wasn't supporting her argument to be considered a full shadowhunter.

"We need to track him," Alec said simply, "We have a rune for that but you need something that belongs to that person."

Clary reached into her back pocket and pulled out her phone. "Yeah well, there's an app for that. And no personal belongings required." Clary tapped at her phone screen for a moment and held up the screen for everyone to see. A map with a grin dot marking the location of Luke's phone came up.

"Tracking runes wouldn't have worked anyway," Jace took the phone from Clary's hand, "He's by water."

"Alright, Jonathan, go change into gear you're coming with Jace and me," Alec ordered, "Izzy you're staying here with Clary."

"I can stay with Clary," Jace volunteered.

 _Of course you can_. Jonathan could tell by the look on Alec's face he wasn't buying it either. "No, you can't. The only people who _haven't_ run off on some sort of adventure with Clary are me and Izzy and I'm not letting you two go without me."

Jonathan had to admit he was a little shocked Alec had agreed so quickly, actually he was more shocked that this seemed to be Alec's idea. "Since when are you so eager to go out on unsanctioned missions?"

Alec didn't look up at Jonathan as he spoke, "Since everyone in this institute seems to have gone mad. Even Hodge is encouraging me to deeper into this before I report anything. Either way I'm getting blamed if this all goes to hell."

"Not hell," Jace corrected, "Just deeper into Brooklyn."

-o.0.o-

Hodge listened from the other side of the monitor to the young shadowhunters plans. He had been hoping Jace and the Lightwoods wouldn't get this involved, but it had been a fruitless hope. Valentine was too big of a deal for them to leave it all on Jonathan and Clary's shoulders. A shadowhunter with unstable health and one without training weren't exactly threatening up against their father.

The sooner he could report this development the better. Hodge slipped out of the control room and into Robert Lightwood's study. Alec had taken to doing some of his work in here while his father was away. Hodge assumed it was so he could imagine himself as the head of the institute when Robert retired.

Other than Alec's occasional presence the room at been undisturbed for the last couple of weeks. He knew he wouldn't be disturbed.

Hodge reached into the pocket of his jacket and produced the ring Valentine had given him years ago. He only used it a couple of times. It was too risky after he had gotten sent to New York. Slipping it onto his finger, he twisted the top half of the ring and thought of Valentine Morgenstern.

Within seconds, a fuzzy image of Valentine appeared in the air by Robert Lightwood's desk.

"Starkweather," Valentine's voice carried a heavy weight even at a hushed volume, "You have something to report, I trust."

"They're on their way to the docks to retrieve Lucian Graymark," Hodge tried to keep the shaking out of his voice but talking to Valentine made him feel like a nervous teenager again, "Stephen and Robert's sons, and Jonathan."

Valentine nodded his approval, things were going his way. "And Clarissa?"

"She's staying at the institute with Isabelle Lightwood," Hodge reported.

Valentine seemed to have expected this, "Thank you for the information Starkweather. Keep tabs on Clarissa for me." The image flickered out and Hodge removed his ring. He didn't know what Valentine was planning but it didn't really matter. It was too late for Hodge to do anything to stop him from moving forward.

 _Remember. It's your way to freedom._

-o.0.o-

Jonathan had heard the phrase "finding for a needle in a haystack" and while it was a lot catchier than "finding one specific shipping container in a sea of shipping containers" he definitely thought the latter was more difficult. Haystacks were at least in a localized location, the shipping containers were stacked for blocks and blocks worth of the port. The app on Clary's phone was only so specific and led them to a specific section of the port but it only helped so much.

"It's really not that large of an area from up here," Jace commented as Jonathan and Alec climbed up on one of the tallest stacks of shipping containers.

"We could probably rule some of them out just from a strategic standpoint," Jonathan said as he surveyed the area around them. He glanced down at his sister's phone and studied the little blue dot on the screen.

Alec stepped up to the edge by Jace, "That's probably a good idea. Anything on the ground is obviously still in play, anything higher up is too difficult to access for it to be worth it."

"It would need to be someplace he could guarantee would be undisturbed for a while," Jace added, "He probably doesn't know how long he'll have to keep Luke here."

"That leaves out any in the small stacks. Larger stacks leave more time before they get to the bottom," Jonathan deduced, "How can we be sure which ones are empty?"

Jace pointed to the north, "The docks don't start until further up the port. I think this is the storage area or something. They're all probably empty."

"Jace, take the stacks to the north and east, Jon, take the south, I've got the west," Alec ordered, "Don't open the doors first, kick at the sides and see if you get a response. There might be things besides hostages hiding in these things. Call if you find anything."

Jonathan pulled his stele out of his back pocket and drew nyx rune on his arm. The dim light of the ship yard shifted until it was brighter. "Don't do anything stupid," Alec called before they split up.

Jonathan jumped down to the alley, holding his hand out to brace himself against the ground. The rune made it easier for him to navigate the dark paths created by the containers. They had used their witchlights on the way in but it had seemed far too bright to him. If he might be going up against Circle members than he needed the upper hand and that meant sneaking around.

The first few containers he checked were empty, after that all the stacks were deemed too short for him to bother checking. He followed the path created by the walls of metal around him like he was in a maze.

There was a strange sense of familiarity washing over him as he walked in the dark. He was used to walking through alleyways to find something to hunt during his patrol. Jonathan tried to trick himself into believing it was just another night but the stab of anxiety in his stomach made it impossible.

He hadn't been this close to his father since he was two. Even if Valentine wasn't physically present Jonathan could feel his eyes on the back of his neck. _He's been watching the institute. He's been watching for me._

He paused to kick one of the storage crates harder than necessary. The bang echoed through the port. Jonathan waited for some sign of a response from the inside. A distant steady beat was barely in earshot. _Footsteps_. He knocked his knuckles against the metal siding just to double check. "Luke?"

The sound of gravel crunching behind him made Jonathan spin around to face the path behind him again. He didn't get to see much before his head was slammed back into the metal wall. His head was spinning and deep back in his skull something was throbbing. He fumbled with his weapons belt for a seraph blade but his attacker took a swing at his jaw, sending his head back into the wall again. His mouth filled with blood.

His attacker wrapped their hand around his neck, not quite tight enough to stop his breathing but enough to make it more difficult. "You're no nearly as vicious as your father says you should be," The attacker growled. It was one of the guys from Luke's Jonathan was almost positive. Even with the nyx rune his vision was black. "Blackwell," He hissed, "Get over here before he passes out. Your father is going to be so thrilled to see you."

Jonathan spat blood in the direction of the voice and vocalized what he hoped was a clever insult but his head was swimming from pain and the blood made his mouth feel slippery. He couldn't even tell if he was actually talking let alone if it was coherent.

He forced himself to get through the fog just enough to see blurry shapes again. His thoughts were sluggish and muddled but it was enough. He spat blood out again, now with a better idea of where his target was. He couldn't see if he hit it but the disgusted groan was answer enough. Jonathan used the moment of hesitation to string one solid thought together. "Fuck you," His voice was barely above a whisper but he felt satisfied with it.

He earned himself one last slam against the shipping container and everything finally went black.


	14. Chapter 14

**Author's note: Sorry my updates are kinda infrequent now. I'm graduating next week so there's a ton of stuff I'm having to do for school. There should be two or three chapters left of this story but I might do a couple epilogues.**

 **WARNING: I DON'T KNOW WHAT YOU GUYS CONSIDER GORE BUT TO BE ON THE SAFE SIDE I'M GOING TO SAY THIS GETS ON THE GORY SIDE AT THE END OF THE CHAPTER I WROTE A SUMMARY OF THE EVENTS IN CASE ANYONE DOESN'T WANT TO READ THAT KIND OF THING**

* * *

When Jonathan came to he was freezing. Where ever they dragged him to, it smelled like decay. He felt a little bit like vomiting but he couldn't determine if it was tied to his withdraw or the pounding in the back of his skull. His arms were hanging at awkward angles, stretched out at wither side of him.

He blinked away the haze blurring his vision. It didn't do much to improve the view. All he had was enough dim lighting to make out he was in a cell.

Chains scraped against the floor as he shifted his legs. He tested the shackles on his wrist, but they were too tight to even be considered breaking out of.

His kidnappers had stripped him of his gear jacket and his weapons belt. Looking down at his chest, he could see purplish red smears staining the grey fabric. "Well that's never going to come out," he grumbled to himself.

Jonathan tilted his head back against the wall behind him. _It was just supposed to be a basic mission. Find Luke. Get in. Get out. That's all it was supposed to be._

He allowed himself to get pissed off. Jace and Alec should have heard the altercation and come running. They should have found him by now. He should have been able to take his attackers. If it weren't for the damn medicine he might have been able to.

Footsteps kept him from dwelling on the elements that caused his current situation for too long. Jonathan tilted his head back down to watch for his approaching visitors. Voices drifted towards the cell but he couldn't make out what anyone was saying.

He squeezed his eyes shut and tried to think past the throbbing his skull. The voices got louder and the footsteps got closer.

"Oh Jonathan," He didn't recognize the voice but he didn't have to open his eyes to know his father was standing outside of his cell, "Rise and shine, my son."

Jonathan opened his eyes slowly. He couldn't see his father's face or the guards standing on either side of him in the shadows.

"Blackwell, we need some light." It was a demand disguised as a suggestion.

Witchlight burned Jonathan's eyes. His eyes watered at the sudden brightness pouring over him.

The cell door creaked as it slid open. Jonathan winced at the sound of his father's footsteps approaching him.

"When I said I wanted him alive I didn't mean bring him close to death was also acceptable," Valentine's voice came from too close. Jonathan strained against his chains to try and close the gap between them.

He didn't know what he planned to do but he knew if he could break the chains he'd get at least one good punch in.

Cold fingers touched his jaw, gently tilting his head to get a better view at the angles. "If it weren't for all the swelling, you'd probably be a good looking young man."

Jonathan wanted to bite his tongue and keep his remarks, he really did, but his father already took away his humanity what else could he strip him of? Besides, who was Valentine to him anyway? He may have been Jonathan's father but he sure as hell wasn't his parent. He was the man that ruined him on a molecular level. "Actually, not at all. Unfortunately I get my looks from my father."

Red hot pain covered the right side of his face as his father's palm slapped against his cheek. Jonathan bit down on the inside of his mouth and blood flowed over his tongue. He locked eyes with his father and spat it on the ground at his father's feet.

He grinned up at Valentine, satisfied with himself.

Looking up at his father he understood why people pointed out the resemblance. It really was uncanny. Jonathan felt like he was looking into a mirror that could show you your reflection at forty.

They shared the same thin lips and slightly pointed nose. The sharp angles of his jaw and cheekbones seemed like they were produced from the exact same mold as his father's. Valentine's skin had start sagging a little with age and stubble peppered his skin but the sharpness was still there. They had the same small eyes only Valentine's had crow's feet attached at the corners.

"I know about you, you know," Valentine said carefully, standing up straight. "About the medications they put you on to undermine everything I did for you. And they still don't treat you as equal do they? Does little, squirrely Hodge Starkweather look you in the eye when you speak to him? Do the shadowhunters visiting the institute look at you like an animal? Do they not all fear the monster you've been hiding from them?"

His father's face split into a cold grin that matched Jonathan's. "I wish you could see yourself right now. Green eyes swallowed in black. Blood almost as dark as demon ichor staining your clothes. Hair dyed the same shade in places," He reached out and put his fingers in a cut at the back of Jonathan's head. A growl ripped out from Jonathan's throat. Valentine's grin widened. "Growling like an animal. Strung up by chains. Blood coating your teeth while you grin like a mad man."

His father knelt down before him again. "Oh Jonathan," He said sweetly, "If only the Clave could see you now. You'd be executed."

Valentine place a hand on Jonathan's knee, he jerked his leg violently but all it earned him was a painful reminder of the shackle around his ankle and a tightened grip on his knee. "I promise you, you're safe here. I only locked you up like this because it's been so long since you've let yourself go completely and I don't think either one of us knows what's going to happen once you do.

"I can see you've already started. Between your eyes and your new aggressive behavior I'd say you're someplace in-between who I created you to be and who they tried to make you into. It probably won't be long before you're back to your natural state." Valentine's grin fell into a blank face as he reached inside the pocket of his jacket. He pulled a syringe of dark liquid out, showing it off in the light. Demon ichor. The same stuff that polluted Jonathan's veins already. "Too bad I was never known for my patience. This will probably hurt, but only a little pinch."

His father hadn't lied. The injection was just a little pinch. It was the way his father had grabbed his hair and jerked his head to the side to stab the needle into his neck that had hurt. The position only got more painful the longer Jonathan was held at the awkward angle.

At first it didn't feel like anything, which was just as surprising as it was unsurprising. Demon ichor could burn holes through gear depending on the type of demon it came from. Jonathan had even seen some pretty bad burns on skin. It never burned him, only made his skin feel a little itchy and hot, like an allergic reaction. He would have thought the straight injection would have at least felt like that, but why would demon blood react to more demon blood?

He wasn't sure but he think it was a full minute before the chill started to spread from the injection site. Jonathan thought he had been cold when he first woke up but it was nothing compared to this. It seemed like forever for it reach his fingers and toes.

Before the cold even spread through half his body his vision started to shift and change. The room rocked some but he knew his head was stationary in the position Valentine had decided would make for the most pain. It was the colors that were changing more than anything.

The cool tint to the witchlight warmed into a light yellow and slowly shifted to a dark red. All he could see of his father's guards were their shadows and those seemed to grow darker.

Next came the tremors. His body started to shake more violently than any withdrawl he'd gone through. The cuff on his wrist rubbed his skin raw as he strained against his restraints, trying to curl up the best he could.

Valentine released his hair once he was satisfied with the results and took a step back to watch his monster of a child react to his most recent despicable act.

Jonathan started coughing. He could still taste the blood from where he bit his cheek, bitter and sour. He could feel the bile rise in his throat and he coughed it up onto his shirt. His throat burned from it but he could still taste the blood. It hadn't tasted this disgusting before. He spat it out again. And again. And again. But the taste was still there, a reminder of what was coursing through his veins.

"I think our work here for tonight is done, gentlemen. Loosen his restraints. Give him some room to walk it off when he's feeling up to standing. He'll be more cooperative in the morning." Valentine turned to walk out of the cell.

Jonathan swallowed against the taste in his mouth. "Clarissa doesn't." His father froze and turned his head slightly to see over his shoulder. It was the exact reaction Jonathan had been expecting at the mention of his sister. His last chance to hurt him in some way. "She doesn't think I'm a monster. That's enough for me."

Valentine was quiet for a long moment. "She's just like her mother," He said quietly. Then with a sharper edge to his voice spat, "She doesn't know any better."

-o.0.o-

The next morning Jonathan had moved himself to the center of the cell. He sat with his legs crossed. His hands rested on his knees and his back as straight as he could make it.

In addition to longer chains on his arm and the shackles removed from his ankles he had been granted a few iratzes. They had felt like a branding iron was being used on his skin. But his bruises and cuts had disappeared and the swelling had gone down. Jonathan thought it was a good trade.

He waited patiently for one of his guards to retrieve him. He hummed to himself, drew runes in the dust on the floor with his fingers. It didn't seem like much time had passed when Blackwell had come to get him.

"Your father wishes you would join him for breakfast." Jonathan got to his feet and held out his wrists to be released. Blackwell made the mistake of setting the handcuffs too high on his arm when he closed them before removing the shackles from his wrists. He probably could have slipped out of them if he wanted, but they would be coming off soon, he was almost positive.

Jonathan was led to an elegantly decorated bedroom. He looked around with disinterest. "You don't intend to have me meet my father for breakfast like this I hope," He gestured to his filthy and torn clothing.

"There's a change of clothes in the bathroom. Clean up and I'll take you to him."

Blackwell grabbed his arm and unlocked the cuffs. Jonathan made a show of rubbing his wrists. "Well this interaction just got a hell of a lot more civilized." He patted Blackwell on the shoulder, ignoring the man's cringe.

Jonathan stepped into the bathroom and stripped off his clothes, leaving them on the floor not sure where to put them and not caring if they were in the right place anyway.

He turned the water in the shower as hot as he could stand it and watched as the water going down the drain went from a dark red to a bright red to pink to clear. He scrubbed the dirt off his skin and ran his hands through his hair until he was satisfied that all the blood was gone.

He changed into the suit his father had provided him. _Only Valentine Morgenstern is pretentious enough to insist on a suit for a father son breakfast_. He thought as he tightened the knot on his tie.

He dried his hair the best he could and combed through it with his fingers. Jonathan deemed himself presentable enough.

Blackwell led him to his father as promised. "Breakfast" turned out to be sitting across from his father with an unnecessarily large desk separating them. There was a tray of tea but no food. Neither one of them moved to touch it.

"Jonathan," Valentine said.

"Father," Jonathan said.

"I need you to tell me everything your sister has told you about the Mortal Cup. Clarissa is the only one who would know where it is. It's very important to my plans." Valentine's voice was reasonable but it grated on Jonathan's nerves.

"Well that will be a little difficult," Jonathan said indifferently, "For starters, Clarissa thinks it's called the Immortal Cup so I don't think she's a reliable source."

Jonathan was already bored with the conversation. He picked a lose thread on his sleeve. "Jonathan this is serious."

"To you maybe. Do you have any scissors?"

"If you don't tell me anything I will have to find your sister and bring her here," Valentine warned.

Jonathan wrapped the thread around his finger and yanked until it snapped. "Well, that would be pointless. She doesn't know. Find her and drag her here or don't, I couldn't care less. What is it that you want the Cup for?"

Valentine looked at Jonathan skeptically, "I'm not falling for that. I'm not giving you that kind of information. You're too docile. You're planning something. You should be acting out."

"And how would you know," Jonathan snapped. "I'm a one of a kind abomination. You don't know how I'm supposed to act. And I'm not planning anything other than ways to end my own life so this boring conversation will end. You want me to act out? Give me something to act out to."

Jonathan got up to leave. "Jocelyn's here," The sound of Valentine's confession froze Jonathan half way out of his chair. "She put herself into some sort of magical coma. I believe she thought somehow it would protect Clarissa. It's got to be just awful knowing she's willing to put her life on the line for her but left you to burn."

The apathy clouding Jonathan's thoughts melted into anger. He kept a fixed look of indifference on his face. His stomach twisted as he watched Valentine evaluate his reaction. The words were supposed to play into a bitterness he had towards his mother. All it did was trigger an anger towards someone else entirely.

Jocelyn may have left Jonathan to burn, but she wasn't the one who struck the match.

* * *

 **Summary: Jonathan is held in a cell by Valentine and Valentine gives him an injection of demon blood to help get the medication out of him faster. Time jump to the next day: Jonathan is pretty apathetic and indifferent to everything even when Valentine threatens to find Clary to gain information about the Mortal Cup. Valentine tries to trigger Jonathan's aggression and anger by reminding him of Jocelyn basically leaving him to die. It works and Jonathan gets upset except it reminds him that Valentine was the one who tried to kill him.**


	15. Chapter 15

**Author's Note: I'M BACK. Sorry for the super long wait, life got chaotic and writer's block is a bitch and I literally had no idea how to write this chapter for like 5 months. I came up with this while sitting in a boring af lecture (it's mainly a transitional point into the climax so it might be kind of boring and too long I'm sorry). The next chapter will hopefully be posted in the next week since I'm on fall break after that there will probably be two or three more updates.**

 **Also I know the timeline is gonna be kind of screwed up because of the "breakfast" scene from the last chapter but since I'm writing this as I post it there's not really much I can do editing wise at this point so I apologize.**

* * *

 **CPOV**

The first time Alec had called, the boys had only been gone for a little over an hour. Isabelle had been helping Clary train as a way to keep her nerves at bay while they waited for any news about Luke when the call came in. She had stepped out of the room to answer the phone and when she came back Clary could tell something was wrong. Isabelle had insisted it was just a routine report.

It wasn't until Alec had called a second time and reported that they had found Luke and were on their way back that Isabelle had finally told Clary what had happened.

Somehow Jace and Alec had managed to lose a six-foot-tall shadowhunter with hair such a bright white it practically glowed in the dark. Alec had heard what he thought was a fight and when he had gone to investigate all he had found was blood on the ground and on the side of one of the shipping containers. Unfortunately, he didn't find her brother.

Clary felt like she was going to throw up. It seemed like every time she got one person in her family back another one was taken away. She was close to having Luke back and Simon was recovering the infirmary, but her mother was still missing and now Jonathan had been taken too.

The wait wasn't making anything better. Alec had told Izzy that Luke was fine, a little bruised up but nothing that wouldn't be gone in a week. Still, every minute the guys took getting back was a minute they could be looking for Jonathan and her mother.

"Aren't Jace and Alec supposed to be two of the best shadowhunters or something? How could they let this happen? They knew there was a risk that our father would be trying to get to us and they still let him go off on his own," Clary complained, "And Jonathan too! He should have known that was a stupid plan. And after all the grief he gave me over the vampire hotel thing! He knows better than I do how dangerous our father is and he still allowed himself to be left alone."

Isabelle sat patiently waiting for Clary to stop her ranting on one of the benches in the main foyer of the institute. "Are you done?" Clary felt like she had summed up her biggest grievances. She gave Isabelle a stiff nod. "You can't hold your brother to the same standards he holds you to. He's been in training since he was a kid, you showed up a couple days ago and learned how to hold a sword. They were probably thinking splitting up would allow them to cover more area.

"Obviously, it was a mistake on their part. We aren't strangers to planning around the _complications_ Jonathan presents during missions, your father was never one we've had to worry about," Isabelle added softly.

Clary knew Isabelle sounded rational but she still couldn't get it out of her head that this was more than just a small mistake. God knows what Valentine would do to Jonathan now that he has him. Jonathan could get killed or worse.

She was about to remind Isabelle of this when the front doors opened and Luke and the two young shadowhunters stepped inside.

Without hesitation, Clary ran over and wrapped her arms around Luke. "Oh thank God," She muttered into his shirt. He cradled her in a tight hug for a long moment while the other three split off to talk in hurried, hushed tones.

One of the boys cleared their throats to get Clary and Luke's attention. "We don't have time for a reunion we've got to come with a plan to get Jonathan back," Alec said. It sounded like he was forcing himself to remain calm. For whatever reason it made Clary furious.

Who was he to call the shots? Odds were it was his orders that got Jonathan taken in the first place. Here he was sounding as indifferent as ever. "I wonder whose fault it is that he's gone at all," Clary muttered.

For a split second Clary could swear she saw Alec's decorum slip. "Excuse me?" He took a step towards her but Jace's hand appeared on his upper arm, pulling him back the few inches he gained.

"We don't have time for petty blame either," Jace at least had the decency to sound a little distraught, and while it calmed clary it seemed to have the opposite effect on Alec.

"The only thing I've done since you've got here is damage control. While you and your brother and Jace have been running all over the city doing the Angel knows what, I've been making sure the Clave doesn't find out about you. Do you have any idea how bad it would look for Valentine to have a conveniently clueless daughter no one knew about show up at the same time he makes his reappearance? If it weren't for me, you'd be getting interrogated or thrown in a cell somewhere."

Clary shrank back into Luke's side as Alec defended himself. In all honesty she hadn't realized Alec was filtering the information he gave to the Clave. She had seen him sifting through file and entering things into the computers once or twice but she hadn't realized what exactly he had been doing. She had just assumed they were normal reports. Maybe they were and he was just editing her out of them.

"If we don't get moving soon all that hard work you did will be in vain," Jace reminded him, "It's going to be hard to cut her out of the story where her older brother gets taken prisoner while trying to track the man that helped Jocelyn evade the Clave for the last 18 years. If we wait too long the Clave is going to _notice_ Jonathan is with Valentine."

The way Jace said it made the weight of the situation worse. It wasn't that they would notice he was gone—it was that they would notice what he was capable of when Valentine was pulling the strings.

"We need to find something we can track Jonathan with," Isabelle joined Jace in trying to diffuse the tension between Clary and Alec. She got up off the bench and started walking in the direction of the residential wing of the institute. "You guys coming? Jonathan doesn't keep his belongings in the foyer."

-o.0.o-

Searching Jonathan's room felt wrong. It was partially because they were invading his privacy but mostly because there didn't really seem to be anything _private_. Most people who had lived in a room for over a decade would have things hidden in places or made the place their own.

Aside from the wooden box of medicine that had been quickly dismissed as an option since Jonathan didn't technically own it, the room seemed like it was inhabited by a visiting shadowhunter, not one that actually lived there.

Clary had been tasked with searching Jonathan's closet. They needed something Jonathan would have an emotional attachment to, something that would really matter to him if it went missing. All of his clothes seemed like standard shadowhunter garb. Black and grey t-shirts, dark jeans and cargo pants.

"Are you guys finding anything?" She called out to the others who were in the process of turning the room upside down. Clary stepped out of the closet as Alec pulled the drawer of the nightstand open and Jace flipped open the cover of a book from a nearby shelf. Something crashed in the bathroom, meaning Izzy had knocked something over.

"Just books he stole out of the library," Jace grumbled as he shoved the book back on the shelf. "Did anyone else notice that Jon has like, no discernable personality or am I really just that self-centered?"

Alec slammed the nightstand drawer shut and sighed in defeat. "You're more arrogant than self-centered." He sat down on the edge of the bed. "I knew Jonathan was careful because of his situation and status with the Clave, but I never realized what extremes he went to. And that's coming from me."

"It really shouldn't be that surprising," Isabelle said as she reappeared in the doorway of the bathroom. She kept her eyes locked on her older brother, "It's one thing to suck up to the Clave to get a promotion, it's another thing to hide parts of yourself so they won't turn on you." Alec stared at his sister for a heartbeat before letting his eyes flicker to the floor.

Everything about the exchange felt like they weren't talking about Jonathan anymore. Clary averted her eyes from both of them, feeling a little bit like she was eavesdropping, and went to sit on the end of Jonathan's bed.

Clary leaned forward, placing her elbows on her knees and burying her face in her hands. "God, this is so hopeless." She couldn't even find something to help her find her brother. The sick feeling in her stomach hadn't faded at all and only got worse.

Looking through Jonathan's things hurt. She remembered seeing the look on his face when he saw the photograph from her first day of kindergarten in the loft. His face had seemed so soft when she told him the occasion for the picture he had seemed confused. Maybe shadowhunters didn't have kindergarten.

He didn't get to have his childhood documented in pictures. He didn't have any posters in his room. He didn't have souvenirs and trinkets lining his shelves. He didn't even have a little box of movie tickets or something equally unnecessary to save. Jonathan had to be careful about anything he owned or showed interest in just so he could stay under the Clave's radar. The things Clary had loved may have been damaged and left behind but at least she had gotten to have them.

A high pitched beeping tone came from her back pocket. Her head snapped up almost instantly. "What was that?" She asked but Jace, Alec, and Izzy were all already checking their phones.

"Not me," Alec mumbled and tossed his phone on the bed. Izzy just shooki her head and tucked her phone back into her pocket.

Jace shrugged and said, "Me neither."

"Wait," Clary remembered that the familiar weight in her back pocket wasn't her phone. She jumped up and pulled the slim device out of her pocket. The bottom corner of the screen had a couple small cracks and the metal around the edge of the phone was a little scratched up. Unlike her phone, it hadn't been protected by a thick case. "Jon and I swapped phones so you guys could use the tracking app." For the first time since the boys had come back she felt hope.

"Clary, Jonathan barely uses his phone," Isabelle began gently, "He wouldn't care if he ever saw it again. It wouldn't work to track him."

Clary momentarily forgot about the shadowhunters' tracking methods. "What? No. Jon still has my phone, or it's at least somewhere in the general area Valentine took him to and that can narrow things down. Luke and Simon both have phones that could let us track it like we did with Luke."

All three of the shadowhunters looked surprised. Jace spoke first, "Who knew mundane technology would prove so helpful?"

-o.0.o-

Luke had gone to visit with Simon in the infirmary while Clary and the shadowhunters tried to find a way to track Jonathan. Simon looked a lot better than when they had first gotten back. His skin looked less pale and he seemed less groggy. Luke was wrapping his own wrist with a bandage when they burst in.

Both of them looked shocked to see the four of them. "Clary-," Luke began but she cut him off.

"Which one of you has more battery left on your phone? It's important."

Simon shuffled through the sheets on his bed until he was able to find his phone. "I don't know what kind of charge it has but it's right here." He offered it to Clary and she took it without hesitation. "Clary, what are you doing? Are you going to find your brother?"

"Trying to," She muttered as she opened the app and tapped on her name. She mumbled encouragements to the phone while the map loaded. "I gave him my phone to track Luke and now we're tracking him the same way."

Before Clary could stop him Simon started to push the sheets off himself. "I'm coming with you."

Clary held her hand out to stop him but he was already swinging his legs over the edge of the bed. "Simon you still need to rest. You were really out of it when we brought you ba—"

He looked up at her with his wide brown eyes—well he looked somewhere slightly to her right. He was still dizzy. "Clary, I'm going with you. You _need_ me." Normally he would have been right, she would need him at her side. But right now he needed to rest more than she needed his support.

"Stand up and walk in a straight line and we'll take you, mundie," Jace challenged from behind Clary.

Simon glared in Jace's general area as he tried to push himself up off the bed. Jace was right, he was too dizzy to even stand. Clary nearly dropped the phone, trying to catch him. Luke helped her get him back on the bed. "Simon," Luke said, "I don't like that Clary is going either but there isn't a choice here."

Clary checked to see if the map had loaded while Luke talked Simon down. She was able to zoom in on the screen until the name of a location appeared near the blue pin representing Clary's phone. "I got a location. Renwick's Hospital in Brooklyn. It's on the outer edge of Brooklyn."

"Wait, Renwick's is a place?" Luke asked.

"Yeah," Alec said, "It's abandoned. Last year we had some problems with the werewolves and the vampires fighting over it. It was getting disruptive and the institute had to intervene. You've heard the name before?"

"The Circle members that locked me up said that's where they were going once they were done with me. I thought Renwick was another shadowhunter."

Clary looked to Jace and the Lightwoods for a reaction. They clearly had history with this Renwick's place and she didn't want to get her hopes just to have them tell her there was another set of hurdles they had to jump over to get there.

Jace and Alec exchanged a look that seemed more like an entire conversation passed between them before Alec spoke again. "Probably your father's headquarters in New York. I'm betting he has Jonathan and Jocelyn there. It's a miracle Jonathan was able to hold onto your phone for that long."

"If this really is Valentine's headquarters we can't just walk in, we need a plan," Isabelle pointed out. "Getting out would be even harder. We don't know what state Jocelyn is going to be in and we definitely don't know what state Jonathan is going to be in. Getting them out could be extremely difficult."

"Alright, we probably have blueprints of the building in the computer system still," Jace suggested, "We could map out the quickest exit routes before we go."

Alec shook his head, "Not fast enough. If Jocelyn is hurt one of us might have to carry her out and we need to prepare for the worst with Jonathan. If he's totally lost it, it's going to take a couple of us at least." He didn't say what they would have to do with Jonathan and Clary was grateful.

"Well do you have a better idea?" Jace was starting to sound as impatient as Clary felt.

Alec looked deep in thought for a moment before he answered. "Yeah actually I think I do," He said as he pulled his phone out of his back pocket. He did something on his phone as he explained his plan. "I don't think getting in is going to be as difficult as we think. It's a difficult place to secure. The quicker the getaway the better. And what's a quicker way to get out than a portal?"

Clary watched as Jace and Isabelle gave each other knowing looks. She felt completely out of the loop. No one had mentioned portals until now.

Alec held the phone up to his ear and waited until the person on the other end answered. "Uh, yeah, Magnus it's Alec Lightwood. Yeah, from the party. No-uh, that's not why- I was calling on the behalf of Clary," He stammered. His cheeks turned faintly pink. "No, the memories aren't the problem. Valentine has Jonathan and Jocelyn and we know where, we just need a quick way to get out once we get them. Yeah, that's what we were hoping. Yes, that will work. I'll let you in myself." He hung up the phone without another word.

Jace and Isabelle were both staring at him, but it was Clary who spoke. "Why do you have Magnus's phone number? Weren't you all weird about going to his party."

Alec's cheeks grew back their pink tint. "He gave it to me at the party," He explained and quickly added, "You know in case you needed anything."

"Right," Isabelle said, clearly not buying it. "Because you and Clary seem so close."

"He's on his way and I need to let him in." Alec's voice made it clear they were done with the conversation. He left the room before Isabelle or anyone else could question him.

"What's Magnus going to do?" Simon asked the question Clary had been thinking.

"Magnus is a warlock so he can open up portals to places he's been before," Jace explained, "If he goes with us to Renwick's he'll be able to open a portal back to the institute that we could put Jonathan and Jocelyn through easily. Quick getaway."

"Clary, can I talk to you for a moment?" Luke didn't wait for her to answer, he just led her out into the hallway. "I can't just let you walk in and confront your father. He's an extremely dangerous man, you do realize that don't you?"

She hadn't really had any interactions with her father, but she heard enough second hand that the idea of coming face to face wasn't exactly comforting. "What else am I supposed to do? If we don't do anything now things could get even worse. As of right now the only thing Valentine has been able to do is make things difficult for us. We don't have any reason to believe he's hurt Mom, but he could really ruin Jonathan's life."

"Clary, you could get seriously hurt."

She felt tears stinging at her eyes. In the last couple of days she had done a lot of things that could have gotten her hurt without giving it a second thought, why should she do it now? What she wanted most at the start of all this was to find her mother and go home.

She knew where to find her mother and realistically, Clary knew that she probably could never go home again. Sure, they could repair the loft and put up new protections or whatever it was that kept her father from finding them for so long, and she could go to mundane school if she really wanted to, but she knew it wouldn't work. She was a shadowhunter now. There was no way she would be able to push this away and pretend it wasn't there, especially if she wanted to still see her brother.

As messed up as their situation was, Clary didn't want to let it go. She had wanted a brother her entire life and one had been dropped right in front of her. It wouldn't be the relationship she always imagined, but there wasn't a single part of her that wasn't ready to fight for it.

Clary had grown up with their mother fighting for her, even if Clary hadn't been aware that there was a fight at all. Since she met him, Jonathan had fought to keep her safe too.

She looked up at Luke, the man that had been more of a father than Valentine would ever be, and saw all the worry in his face. "I have to do this. I have to fight for them."


	16. Chapter 16

**Author's Note: This is the chapter is the climax, it's a little violent towards the end. After this I'll write one or two more chapters. I'll see how they come together once I get to writing them. I'm trying to come up with another multi-chapter fic to do next. Thank you for 100 Followers by the way!**

 **Please review!**

* * *

 **Jonathan's POV**

They had been staring at each other for quite some time without saying anything. Valentine was studying Jonathan carefully. Jonathan felt more than just agitated but he tried his best to keep it from showing. His father was waiting for any sign that he was losing control. He refused to give him any, it was much more fun watching him grow paranoid.

When he started to get bored Jonathan spoke louder than he needed to. "How did it feel?" He asked. He hid his smile at the slight jump of his father's shoulders.

Valentine took a moment to regain his composure. "How did what feel?"

"Starting the fire," Jonathan cocked his head to the side and watched for his father's reaction. Valentine was almost as good at Jonathan at hiding his emotions. Must be genetic. "You know, setting a house on fire with your child inside."

Valentine's jaw tensed but he didn't respond.

"I'd say that there must have been some part of you that didn't want to do it but I think we both know I would be giving you too much credit." Jonathan shifted in his chair to get more comfortable. "People think I'm sick but at least I'm the product of a horrific experiment. You didn't even need the demon blood, you're just like this."

Valentine stood up, slamming his hands on his desktop. Jonathan didn't even flinch. He had been waiting for that exact reaction and it was even better than he had hoped. He could tell his father regretted ever bringing him here. As useful as Valentine thought he could be, it was clear he didn't think it was worth being disrespected by his son.

Jonathan felt satisfied. He sat back and waited for his father's scolding to begin.

Before Valentine could tear into Jonathan the door of the office opened. Valentine's anger seemed to melt away, and the calm, respectable leader he had convinced his followers he was. Jonathan craned his head to see which Circle member was standing in the doorway. Blackwell.

The Circle member appeared sweaty and out of breath. "Sir, someone's infiltrated the building."

Jonathan knew exactly who would be capable and dumb enough to try that. Things were about to get a lot more interesting. "Uh-oh," He grinned at his father, "Looks like _you_ spent too much time playing mad scientist."

Valentine's composure almost slipped. He didn't let his eyes slip to glare at Jonathan. "Thank you, Blackwell," His father's voice was tight, "You are dismissed."

Within seconds of Blackwell shutting the door behind himself Valentine was on the other side of the desk, standing in front of Jonathan.

Valentine put him in a position similar to the one he had him in the cell, fingers knotted in his hair and neck bent at a painful angle. He lowered his face until he could whisper in Jonathan's ear, "Believe me when I say that the second your sister and the Lightwoods see you they're going to believe you're on my side whether you have agreed to be or not. They're going to see those black eyes and they're going to start planning ways to take you out. Your instincts are going to react to the threat and one of two things will happen: you're going to just let yourself go or you're going to get in your own head and slow yourself down. It _will_ make a difference. Either kill or be killed.

"You're not going to be able to stop yourself. You may hate me, but I'm not the one who will be trying to kill you. You have a side to choose," Valentine released him and straightened his posture. He pulled something out of his jacket pocket and dropped it in Jonathan's lap. An overly ornate silver dagger laid across his knees. Jonathan didn't move to touch it. "Choose wisely."

Valentine started walking towards the door, leaving Jonathan motionless in his chair. It only took Jonathan a few seconds to decide to take the dagger. He wrapped his finger around the grip and followed his father.

His father had made appeal after appeal to Jonathan and it had finally worked. Self-preservation was something shadowhunters and demons had in common.

"Where are you keeping my mother?" Jonathan asked after he caught up with Valentine. Jonathan didn't give him much time to respond. He saw the slight movement of the corner of his father's mouth and knew no matter what came out of Valentine's mouth it wouldn't be a real answer. "I'm not going to go after her if that's what you're worried about. In case Cl-" He stopped himself before he gave his sister away. Sure he knew who had intruded but Valentine might not have made the connection yet, "The intruders are looking for her. I can lead them astray."

"Even if I was looking to attack Jocelyn, you were the one that offered her up as bait to see if I would react," Jonathan kept his tone light and conversational. It seemed to make his father more uncomfortable the more pleasant he sounded. Even though he didn't feel much of anything it was surprisingly easy for him to keep the emotion in his voice. "You have a pretty messed up way of expressing love by the way."

"She's in the east wing of the second floor, if you must know." Valentine stopped walking suddenly and tugged the door of a new room open. It looked like a waiting room. One of the walls was lined with broken and filthy chairs, another had a cut out in the wall that looked into some kind of office. _It's an old hospital._ There hadn't really been anything in the other parts of the building he had been in that seemed as distinctive. Just a lot of empty hallways with lots of doors.

It didn't take long for them to hear the sounds of fighting coming from a doorway on the opposite side of the room. Jonathan was struck by how calmly his father stood waiting. "You were expecting this, weren't you?"

"I've heard how much your sister is like your mother," Valentine said without looking away from the doorway. He reached into his jacket and pulled out another dagger, similar to the one he had given Jonathan, "I knew taking you would make her all the more motivated to find me. Best case scenario, you would have information on where to find the cup and I wouldn't need her at all. It would make the fight a lot less complicated if we weren't worrying about capturing one specific person.

"I wasn't sure how many your friends your sister would bring. I didn't think it would be many. Still, getting her isolated and out of the melee unharmed is going to be difficult. Watch for any openings."

Jonathan raised his eyebrows, Valentine _did_ know it was Clary. He had planned for it to be Clary, "I was the bait?" It was the only part of Valentine's plan that had stuck with him. "All I am is the damn bait and you still put me through hell for nothing?" The edge to his voice was undeniable, but he couldn't find it in himself to be ashamed of it. He was furious and in this state there was only so much he could do to control it.

"It wasn't for nothing," Jonathan could see the smirk on his father's face even from the side, "By forcing you to give into your true nature I've isolated you too. You picked up that dagger because you knew I was right when I told you that they would fight against you. I was successful in forcing your hand in this fight."

The sounds of the fight from the hall grew louder before dying out completely. Jonathan heard a familiar voice call out orders and the sound of footsteps running up the hall. It was only a matter of seconds before Alec appeared in the doorway.

He didn't notice Jonathan and Valentine at first, he was too busy looking to see if the others were following.

Jonathan felt himself tense all over. That was a mistake. Alec knew better than to stop like that. He should have checked the room. If it hadn't just been Jonathan and Valentine in here he would have been taken out in seconds.

A heartbeat later, Alec looked over and saw who was waiting for them. His eyes widened and he reached for one of the arrows in the quiver strapped across his back. His eyes were set on Valentine. It wasn't until Jace appeared at his side that they flickered towards Jonathan. If seeing Valentine had been a shock for Alec, seeing Jonathan was even more surprising.

Jace gestured for someone to stay back with one hand and gripped his seraph blade with the other. _Clary_. Jonathan's grip tightened on the dagger. His head was starting to hurt. The rage he felt towards his father was conflicting with something else inside him but he couldn't wrap his head around what he was feeling.

He felt like there was something he should have done differently. It must have been the dagger. He had taken it and in doing so he had played right into his father's hand. If the black eyes weren't enough to make him look guilty, the dagger definitely did the trick.

Jonathan looked guilty enough Jace was telling Clary to back down. He didn't want her to see her brother like this. _Like the monster everyone is afraid of._ It was only a matter of time before they turned on him just like his father had said.

He knew Valentine was a master manipulator, that's how the Circle got so large and powerful, but even this was impressive. There were parts of Jonathan that were just as calculating as his father. The idea made his head hurt even more.

"Don't," Jace hissed to Clary and whoever else they brought. The order didn't stick and Jonathan saw a flash of red hair. Isabelle and Magnus appeared in the doorway behind his sister.

Jonathan looked down at the dagger, it was completely still even if he felt unsteady. He glanced back up and Clary was standing there watching him. Watching him with wide green eyes. The dagger felt heavy.

Valentine took a step forward, Jonathan didn't know if he was going to try and instigate the fight or give a speech. With his father it was difficult to tell. Either way Jonathan only had a few more seconds to use his father's manipulation against him and turn the tables.

"Father," Jonathan stepped forward until he was standing right next to Valentine. He ignored the way his friends tensed. "Do you remember earlier when you told me my instincts would kick in once I was threatened? That my sense of self-preservation would take over and I would either kill or be killed?"

"That was ten minutes ago, Jonathan, now really isn't the time," Valentine scolded.

"I just wanted to let you know you were right," Jonathan continued like his father hadn't spoken, "And that I did have to make a choice."

Valentine turned to smile at his son, "I think we all know you made your choice." He held up the dagger he was holding as a reminder of the one in Jonathan's hand. Upon closer inspection it really was identical to Jonathan's.

Jonathan angled his body so he wouldn't have to look at Clary or the others when he made his next move. He could still feel all of them watching. "I chose kill." He reached up and slammed his empty fist against father's wrist. His weapon fell to the ground and Jonathan plunged his own into this father's chest. He heard Clary's strangled cry from someplace far away.

Valentine nearly stumbled back with the force of the blow. Jonathan's arm wrapped around him to keep him standing. He lowered his face so he could whisper in his father's ear. "It's your turn to burn."

He pulled back, his father's eyes were wide and shocked. "You'll always be a monster to them," Valentine spat out around the blood pooling his mouth.

"Probably," Jonathan conceded, "But at least I won't be your pet." Jonathan pulled the dagger back out, pursing his lips with the effort of supporting his father's weight while he did so. He had missed his target the first time, it was a good hit but not far enough to the side. Again Jonathan's hand came down and he felt the dagger hit his target, his father's corrupt heart.

He watched and waited as his father struggled and gasped for a long minute. When Valentine's eyes finally went blank Jonathan let him go. The body feel onto the dusty ground with a sickening thump. Jonathan stared down at it. His head didn't hurt anymore.

"Jon?" It was Isabelle's voice. "Jon, are you okay?" She spoke softly, like he was a stray dog she wasn't sure had rabies.

Blood seeped out onto the floor by his father's chest. "He was right," Jonathan's voice sounded hollow even to his own ears. "Everyone's always going to look at me like I'm a monster. Treat me like an animal." His eyes flickered up to Isabelle for a fraction of a second.

"And it's his fault." Jonathan tapped the body with his foot. "It's all his fucking fault."

Something finally snapped inside of him. That last lingering thread of control was gone. He knew in some ways he was letting his father win but he couldn't bring it in himself to care. All he felt was fury.

He kicked his father's body over and over and over again, muttering curses and accusations.

"Jon stop!" Clary screamed. Jonathan ignored it and kept going. He was finally fighting back.

"Izzy, Magnus, get Clary out of here," Jace ordered.

"Get him on the right side," Alec called, "I got his left."

Jonathan didn't fight against Alec and Jace when they grabbed him and started hauling him backwards but he didn't stop kicking in Valentine's direction either.

"Hold his head still, I'll put a sleeping rune on his neck," Jonathan didn't care who said it but it made him go still.

"Wait," Both Alec and Jace's grips tightened on Jonathan's arms. Alec even went the extra mile to pin his arm behind is back at an uncomfortable angle. "Clary!" Magnus and Isabelle had gotten her out of there fast. He felt something that might have been relief but he was having to hard of a time keeping his head straight. "Clary! Second floor! East Wing!"

"What's on the second floor?" Jace paused with his stele half way to Jonathan's neck.

Jonathan rolled his head to the side, giving Jace access to a bare spot on his neck. "Jocelyn." Jace and Alec both stiffened. "Just knock me out already," He growled, "Before I get out of hand again."


	17. Chapter 17

**Author's Note: Super long update because I couldn't find a good place to stop. Please review :)**

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Sluggish didn't begin to cover how Jonathan was feeling. Getting back on his medication had been harder than anticipated for a variety of reasons. The injection his father had given him was fighting against the ones the Silent Brothers were giving him. His mood would be stabilized for a couple hours before the effects would fade and he was back to his natural state.

He hated thinking in terms of his "natural state" versus his "rational state", but more than anything he needed to be honest with himself. The demon blood would always be in his veins even now that the booster his father had given him was nearly gone. That fact had been shoved in his face repeatedly over the last few days of interviews with Clave officials.

Jonathan wasn't proud of letting his natural-self take control the night he killed his father, but he felt the Clave should at least offer a "thank you" for taking out their number one most wanted. Instead they put him through a very long series of interviews that were meant to find out if under his medication he should still be allowed to serve alongside other shadowhunters.

Yesterday, four long days after that night, the Clave had reached a conclusion that he could return to business as usual for a two-month trial. After that, they would make a final decision. In the meantime, he had to be on his best behavior.

It wouldn't be difficult. He wasn't in any condition to be causing any trouble. His muscles were sore and getting back on the medication was disorienting. He had spent a lot of time in his room to recover. Isabelle and Jace had both stopped in a couple of times to give him updates. Apparently, the Lightwoods' parents were back and had taken over the institute from Alec. They weren't happy with all the trouble and complications they had caused, but like almost every shadowhunter, they were relieved Valentine had been stopped before things got worse.

Jonathan hadn't gotten to see Clary since that night, in all honesty he was a little scared to. She called him the night before using Luke's phone since she hadn't gotten around to replacing the one that was left someplace in Renwick's. She wanted to meet him for lunch at the café they had met Simon at.

He stayed in bed as long as he could before he had to get ready. He was just pulling his shirt over his head when someone knocked on the door. "Door's open!" Jonathan called as he readjusted the hem of his shirt.

Of all the people he was expecting to walk through his door, Magnus Bane was not one of them. Alec following along behind was nearly as surprising. Alec and Jonathan only interacted when it was absolutely necessary, they did live together so it seemed slightly more reasonable that Alec would stop by to check up on him.

"Uh, hi?" Jonathan said while Alec shut the door behind himself. "What's going on?"

Alec held out a folder with the Clave seal on the cover. Jonathan swallowed a groan and let his head fall back. "Seriously? I have to do paper work on this shit too?" He took the folder from Alec and opened it up, expecting some blank forms he'd have to fill out, instead the first page was entirely small print text. He flipped through more to find they were all identical.

The last page had three lines and spots for dates. Two of the lines were already filled with looping script. Magnus Bane and Lydia Branwell. Jonathan looked up from the folder at the two men standing in his room. "What is this?"

"While you were—uh— _recovering,_ Magnus asked me to help him draft a proposal for the Clave," Alec explained. It was a vague explanation, and Jonathan still didn't understand.

Magnus rested his hand gently on Alec's shoulder. Alec visibly tensed and his cheeks turned slightly pink. "I wanted to offer my services to you, free of charge. I knew that I would have to ask the Clave's permission before I formally offered it to you and Alexander helped me with all of the legal jargon." The look on Jonathan's face must have made it obvious that he wasn't catching on as fast as Magnus was wanting.

Magnus let his hand drop from Alec's shoulder—Alec's exhale was audible. He took the file folder out of Jonathan's hands. "This is a contract constructed by me and Clave representatives that would allow me to block your memories from the other night," Magnus explained. "It's a similar spell to the one I put on Clary's mind. Instead of filtering the way your mind remembers things it'll block those memories entirely. When you try and think back to that eighteen hours you won't be able to remember anything.

"It's painless. It can be reversed at any time. A Silent Brother has to be present when I cast the spell and I have to provide a way for them to access the memories in case they need them. I can't guarantee that if the Silent Brothers do at some point in the future poke around in that strange head of yours that it won't cause some of the memory to leak out. If that does happen can repair it." Magnus bent the pages of the contract back until the signatures were front and center. He snapped his fingers and a pen appeared in his hand. He offered it and the contract to Jonathan.

There was probably a good first reaction to this kind of offer but Jonathan could not think of what it was for the life of him. Instead of taking the pen and signing he just stared at Magnus and asked, "Why?"

Magnus lowered the contract and pen. "I'm offering a thank you on behalf of the downworld. We've seen what your father was capable once before twenty years ago. Believe me. None of us wanted a repeat. It wasn't just the Nephilim you saved, Jonathan."

Jonathan stared at the contract in Magnus's hand. The worst eighteen hours of his life could all be locked away in a small little part of his mind. As appealing as the offer was, something major had happened in that eighteen hours, something Jonathan would hear about for the rest of his life. "What happens if someone mentions it to me? Is everything just going to come undone?"

"It'll be like someone mentioning something that happened to someone else. You can acknowledge it, but you won't remember that it happened to you." Magnus held out the contract again and this time Jonathan took it.

He didn't sign it, but he did take it. "Is there an expiration date?"

"No, but you will have to come see me every few years to make sure it's still working sometimes the-," Magnus started to answer.

"Not the spell, the offer," Jonathan clarified. "Is there an expiration date on the offer?"

"The Clave didn't give us one exactly but it was strongly implied sooner is much better than later," Alec answered. Alec tucked his hands into his pockets. "I mean do you really need to think about it? Erasing one of the most traumatic moments of your life?"

Jonathan shrugged. "I don't know," He guessed he should have been grateful for the opportunity it just felt a little weird. "I'm just not sure how to feel about other people remembering it when I can't. Can I keep this until I'm ready to sign?"

"Sure," Magnus gave him a sad smile. He must have not expected this to be such a difficult decision for him to make. Jonathan appreciated the gesture and the motivation behind it but this was a big decision. "Alexander has my phone number for when you make a decision."

Magnus and Alec left him with the contract. As soon as they were gone Jonathan tucked the contract into his nightstand. This would have to be something that he would deal with later, he was already running late.

-o.0.o-

Thankfully, this time there wasn't anyone spouting bizarre poetry on the stage in the corner of the café when Jonathan arrived. Nearly all of the tables were occupied, and there was a short line at the counter. It was easy to spot Clary's bright hair from across the room.

He slid into the chair across from his sister, startling her attention away from the drawing she was doodling on a napkin. "Please tell me I'm not super late," Jonathan begged even though he already knew it was twenty minutes past the time they were supposed to meet.

Magnus's offer had taken a good ten minutes, and a delay on the subway had added another ten minutes to his route.

Clary smirked and went back to adding details to her drawing. "I'm only letting it slide because I just got here five minutes ago."

Jonathan relaxed back into his chair. "Good because my excuse was going to be that I couldn't find you in this crowd, but that doesn't exactly work with your hair."

"The same could be said for you, big brother. Here," She set the napkin in front of him, "Have a kitten." The drawing was a little smudge as a result of the canvas it was painted on but it was still a cute kitten curled up sleeping. She had even signed the corner in overly loopy letters.

It only took a couple minutes with his sister to make him feel better than he had in days. Clary didn't want his statement or his signature on a contract. She wanted him to have a drawing of a napping kitten. "A Clary Fray original? This could be _really_ valuable one day."

"As long as you don't accidentally throw it away," Clary warned. Jonathan kept eye contact with her as he folded it up and put it in his breast pocket. His sister seemed satisfied. When she spoke again her voice was softer, "Are you doing okay? I haven't been able to get to the institute to check on you."

"If you had stopped by I doubt I would have been able to see you. I've been kept pretty busy." Jonathan thought about telling her about Magnus's offer but changed his mind. That was a decision for him to make on his own. He didn't think Clary would try and influence his choice but he knew she would have opinions. "It took a little way for the medicine to start working right, but I think I'm good now. Are you okay after, uh, _everything_?" _After watching me brutally murder our father._

Clary tapped her pen against the table top. "It's been," She paused to think of the right word, "A lot. I haven't been sleeping well, but I think that might have more to do with all the crappy hospital coffee I've been drinking than the _other stuff_. Speaking of coffee, I need some that's not burnt, want anything?"

"Just get me one of whatever you're getting."

Jonathan knew that they had taken Jocelyn to a hospital where one of Magnus's friends worked. He didn't know Clary had been there too this entire time. He felt a little guilty about not asking about it. He wasn't used to thinking about his mother as part of his life.

Clary came back and set a mug of black coffee in front of him. "How's Jocelyn doing?"

"She finally woke up yesterday morning. She's a little disoriented and obviously dehydrated and that kind of stuff so she'll be in there a couple more days." Clary blew on the top of her coffee. "I thought I would be angrier than I was. I mean, she lied to me for eighteen years and messed with my head and all kinds of stuff but I was just so relieved she was okay. I'm sure we'll fight about it later but for right now I'm just glad to have her back."

Clary smiled down at her coffee. "Wait, are you busy for the rest of the day?"

"No," Jonathan knew he should probably get back to the institute and read the contract in his nightstand. Just taking the time to think it over so he could get back to Magnus and Alec with his final decision.

"You should come to the hospital," Clary's eyes lit up, "You could meet Mom."

Suddenly Jonathan really wanted to be back in the interrogation room. He wrapped his hands around his mug of coffee, letting the heat burn into his palm. He stared at the dark coffee to avoid meeting his sister's eyes. "Clary, I don't know if that's such a good idea. I-I don't know if I'm ready for that."

"I know it's going to be difficult but don't you think it will kind of be a Band-Aid situation? Oh wait shadowhunters don't use Band-Aids. Do you know what I mean by 'Band-Aid situation'?" Jonathan glanced up while his sister was babbling and nearly burst out laughing at the confusion on her face. "I don't really know how else to explain it."

"I know what you mean. Do it fast and it will hurt less," Jonathan assured her. He looked down at his hands again. "That may be true but that doesn't mean that I have to do it anytime soon."

"Yeah, but don't you see that the sooner you do this the sooner you both can start healing from what he did to this family?" Clary's voice was getting louder. Jonathan glanced around them to see if anyone was noticing. He didn't really want to have any discussion about their father in public. "I mean there's nearly two decades of memories he cheated us out of. You and Mom don't have any relationship whatsoever all because of him. He's gone now Jonathan. He can't hurt you anymore."

Jonathan didn't look at her. All he could see was the bloody dagger and his father's body. Magnus's offer grew more appealing with each passing second.

"Jon, please." Clary reached out and took one of his hands in hers. "At least try. If we get to the room and you don't want to go in that's fine. You can wait outside and while I say a quick hi. Then we can go to the loft and you can keep me company while I pack up some stuff."

"Fine," Jonathan knew he wasn't going into the room, but maybe he'd get a sudden burst of courage and face his mother head on. "I'm not making any promises."

-o.0.o-

Mundane hospitals reminded Jonathan of the institute. On the floor Clary took him to there was a large desk area with lots of computers and a common waiting area with chairs and tables. Hallways of patient rooms seemed to branch off in every direction. People were running around with files, some of them busy reading them as they walked. It was the type of chaos and hustle and bustle that Jonathan was used to.

The familiar feeling of the building did little to dull Jonathan's nerves. There was no way he was going to be able to face Jocelyn today. He had spent the entire time in the elevator up with his eyes closed, focusing on controlling his breathing.

Clary pulled him to the side as he started walking towards the front desk. "See that nurse? She can't see that I'm taking you back to the room. So just hang on until we can get passed without her seeing."

"Why?" Jonathan didn't know much about mundane medical care, but he felt like sneaking into a hospital wasn't a thing people usually did.

"Because," Clary peeked around him to see if the nurse was watching, "When Mom was asleep I was the one who confirmed her visitors were in fact family, now that she's awake that's her job. Since she hasn't seen you since you were two she won't really be able to confirm it. Well, maybe she could with the eyes it's kind of a dead giveaway, but her shock at seeing you probably won't make her sound convincing. Okay let's go."

Clary moved to dart across the room but Jonathan caught her arm. "Clarissa," He could hear himself channeling Alec's big brother voice, "Does Jocelyn know I'm alive?"

She looked at every place around his head but never met his eyes. "Uh, she knows I know about you."

Jonathan set his hands on her shoulders, "Does our mother know that I am alive? Yes or no."

"Not exact—"

"Yes or no."

"Okay no, but I—"

He dropped his hands from her shoulders and started backing up towards the elevator. "Bye. I'll call you on Luke's phone later," Clary tried to interrupt but he talked over her, "I'll tell Jace that you want some help packing up stuff. I'm sure he'll jump on the chance to spend some more time with you now that this is all over."

This whole trip felt like a trick. Jonathan had reservations about this plan when he thought that Jocelyn _knew_ he might stop by or was at least capable of doing so had been strong enough, there was no way he was going to blind side her. There's no telling what her reaction would be if she didn't have time to prepare. Jonathan had imagined a few ways she would react, and he didn't think he'd be able to handle most of them.

As Jonathan pressed the down button for the elevator Clary closed the gap between them and tried to tug him back towards the desk. "Jon listen, Luke figured it was for the best not to tell her right away. We were going to tell her later today. She'll want to meet you."

Jonathan spun around to face her. "You don't know that, Clary. You can't just spring this on her."

"It's not like you're asking her for anything. You're just introducing yourself."

"But I am asking for something," How could she not understand the risks of this? "Just by showing up I'm asking her to face a lot of stuff she'd probably like to forget. I'm not doing this Clary. Tell her the truth and I will consider it."

"What about moving on from everything that's happened?"

Memories of the other night came bubbling back but Jonathan squashed them down. "Look, this seems really important to you and I have a feeling it means something different for me. You do whatever you think needs to be done so _you_ can start healing or whatever and I'll do what I have to do."

Jonathan stepped back onto the elevator and refused to look at Clary. "Jonathan, I'm sor—," but the doors closed and cut off her apology.

It took exactly one floor for Jonathan to make his decision. By the time he was off the elevator he had called Alec to let him know he'd sign the contract as soon as he was back at the institute. He wanted this done and he wanted it done before he could talk himself out of it.

Clary was right. He needed to find a way to move on, but it had nothing to do with Jocelyn. He had worked hard his whole life to suppress the demonic side of him, and he had been pretty successful up until his father forced his hand. He needed Magnus's magic to help him keep that night from interfering with all the work he's put in.

-o.0.o-

"Have you told anyone about this?" Magnus asked as he set up his spell book on the table next to Jonathan. "Clary? Isabelle? Anyone at all?"

"You, Alec, that Clave rep, and Jerimiah over there are the only people in the know," Jonathan nodded in the direction of the silent brother sitting quietly in the corner of his room. With the stiches over his eyes and mouth and the way the lighting hit him, he looked like something Jonathan would be having nightmares about later.

Jonathan knocked his fist into the arm of the chair Magnus sat him in. "This is my decision. I made it on my own without anyone else's influence. This is for me." He didn't sound as confident as he wanted to.

Magnus stopped looking over his book and looked down at Jonathan. "I'm going to be honest with you, I spent quite a few decades after I found out what I was to reconcile that there was a part of me that was demonic. It makes you question a lot of things about yourself." It was strange hearing Magnus speak so candidly. A week ago Magnus Bane was nothing more than a name and a reputation that made him sound almost fictional. Now he was standing in front of Jonathan talking about his past. "To put this bluntly you don't have the kind of time I did, so I'm going to let you in on a little secret.

"You're allowed to want and do things that benefit you and you alone. Even if it ends up making someone else upset or hurt. No one can spend their entire life walking on eggshells. Stepping off them doesn't mean you're tapping into the demonic side of you, it means you're being human."

Jonathan swallowed. "It's easy for you to say that," he said in a low voice, "The demon part of you gives you powers and stuff that's beneficial. Mine makes me kill people. All it does is hurt me and other people."

"The only thing besides a demon you ever killed was a man who killed a lot of other people and planning to kill more. If that's your worst act on your worst day you're doing pretty good."

It was a valid point, Jonathan just wished he could convince himself to believe it. He knew that this spell wasn't going to magically make him okay with what he did, but at least he wouldn't remember it anymore.

"Now," Magnus picked his book up and rested it on his arm, "Are you ready?"

Jonathan barely nodded his head in response. Jeremiah got up out of his chair and approached slowly.

 _You may begin at any time, Magnus Bane._ Jeremiah's voice echoed in Jonathan's head.

"Yes, watch carefully because I'm not going to be able to do this twice." Magnus snapped his fingers and blue light appeared in the air around them. "Jonathan, I want you to close your eyes and think of the moment you were captured. Go step by step through your memories. I'll tell you when to stop."

Jonathan did as he was told. It was harder than he thought because he could feel Magnus's magic building up as he continued through his memories. On more than one occasion they had to slow things down or pause completely so he could figure out where he was. Jonathan had to ask Magnus a couple of times to prompt him.

"Alright, open your eyes." Magnus and Jeremiah were both staring at him—well Magnus was, Jeremiah's head was just pointed in his direction. "Can you remember killing Valentine Morgenstern?"

Jonathan tried to think back but it was like his mind hit a wall. All he managed to think was blackness. He shook his head, "No, I don't." He couldn't even remember how Valentine had died just that he was dead.

"What is the last thing you remember from Sunday night?"

Jonathan looked at the ground in between Magnus and Jeremiah's feet. He retraced his day through his head until he hit the blackness again. "We were checking the shipping containers. We thought it would be better to split up, but I don't remember what happened after that." The memory was gone. It wouldn't be sneaking its way into his thoughts anymore. He looked up at Magnus. "It worked. It actually worked."

He could feel the stupid smile spreading across his face, but he didn't want to stop it.

"As if there was any doubt," Magnus closed his book with a loud snap, "Let me know if you discover any holes. There won't be any, but just in case. Well Jeremiah let's leave the boy to enjoy his ignorance."


	18. Chapter 18

**Author's Note: This is the final chapter of my first fanfiction. I wish I could have ended it better but I was like half a page away from being done with this for over two months so I figured I needed to just hold my breath and write something to finish it up. I apologize if the last page worth or so isn't that satisfying, but I think I got the conversation I wanted to write out there.**

 **Thank you to everyone who commented/favorited/followed. You have no idea how much the feedback means to me.**

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Jonathan never thought he would be grateful to go back to his normal schedule, even if it meant getting his ass handed to him by Jace during training. This was the third time he landed flat on his back, and the training mats were doing next to nothing to cushion the marble tile underneath. He tried his hardest to suck air back into his lungs.

"So you just don't remember _anything_?" Jace offered his hand and Jonathan used it to pull himself to his feet.

Jonathan picked his bo staff back up off the ground. "Pretty much. Like Imagine reading a book and skipping like three or four chapters in the middle. That's kind of what it feels like. I know what happened before and what happened after, but the only thing I know about the middle is the bits and pieces people bring up now."

Jace thought about the comparison for a moment before nodding. They both moved back into fighting stances. "And you told Clary all of this over text message?" Jace lunged forward but Jonathan blocked his strike. "That seems like it should be a face to face conversation."

Jonathan preformed a combination of moves. Jace was able to counter each one but he still had to take a step back. "Not her mind. Not her say." Jonathan tried to kick Jace's foot out from underneath him, but Jace side stepped it easily. "And I'm still a little mad at her."

"Clary was just trying to help," Jace pointed out as he aimed a hit at Jonathan's shoulder. The blow echoed pain down his upper arm, but he was able to keep his hold on the staff. "She wants you to be able to move on. Isn't that what you were doing when you had Magnus do his thing? Finding a way to move on?"

"Remember when I said I was cool with you dating my sister?" Jonathan blocked another blow from Jace, "I'm going to take that back if you keep taking her side."

"Too late, I'm taking her out tomorrow." Jace made a move that cost Jonathan his grip just as his phone beeped on the other side of the room.

Jonathan held his hands up in a silent sign that he was ready for a time out. Jace nodded in the direction of his phone. "I'd rephrase that next time," Jonathan picked up his phone, "When trained soldiers say they're 'taking someone out' it usually means something a little different than what you just said."

"Noted." Jace picked up Jonathan's abandoned bo staff and put it back on the rack.

A new text from Luke was waiting in Jonathan's messages.

 _I'm sorry about the other day. Mom and Luke are out. Do you want to come over to Luke's and order in? My treat. –Clary_

He read over the text message a few times before deciding how to respond. It had been two days since he left Clary at the hospital. Of the two uncomfortable situations he was avoiding this one was probably the most unnecessary.

 _Fine. I need to jump in the shower first. I'll be there in an hour._

"Hey, I'm going to Luke's to hang out with Clary," Jonathan tucked his phone in his back pocket, "I'll be back by eleven in case I'm actually allowed to patrol tonight. Let the Lightwoods know for me?"

Jace paused folding up the training mat, "Sure. Tell Clary I said hi."

-o.0.o-

It was only a little over a week ago that Jonathan had visited Luke's house for the first time but it felt like months. Hopefully, he wouldn't be pinned to the ground this time. Less jumping out of windows would also be nice.

He jogged up the front steps of Luke's stoop and rapt his knuckles against the wood of the door, hoping Clary would be able to hear him. Luke's house seemed a lot less daunting under today's circumstances. The blinds in the front windows were open and he could see the light of a television set. The never had one at the institute, but a couple of the bars they stopped at on patrols had several mounted in the place.

Jonathan felt his phone buzz in his jacket pocket. Another text from Luke's phone.

 _In the middle of something in the kitchen. Can't get the door. It's unlocked. –Clary_

He tried the door knob and pushed but the door stuck. He remembered Clary's trick from his first visit. Jonathan lined his shoulder up with the right part of the door and slammed his side into it. Shadowhunter training and demon strength kicked in and made him overestimate the amount of force. He stumbled into the foyer with the door.

He froze briefly, checking the surrounding area to see if anyone had noticed. True to Clary's word, Luke and their mother were nowhere in sight. "Clary?" He called after closing the door.

The sound of a refrigerator door being slammed answered him. Last time he was here, Jonathan didn't get too much time to memorize the floor plan, mostly because he spent so much time on the floor. He went in the direction he felt the sound had come from.

"Clary?" He called again as he crossed the threshold into the kitchen. He saw a glimpse of red hair out of the corner of his eyes. "Hey, you really shouldn't leave the door—"

It wasn't Clary in the kitchen. His mother was in the middle of putting dishes away. She really did look like Clary. Or more accurately, Clary looked like her. Same red hair and curls, same face shape, same nose.

The same eyes.

Jonathan didn't move. "Unlocked?" Jocelyn finished his sentence for him while she closed the cabinet door. She straightened up and smoothed her shirt. Tiny flecks of paint dotted the hem of the blue button up. "Clary told me about your argument. I thought I'd take matters into my own hands and send you those texts. I've lied so much, I figured one more small one wouldn't make much of a difference"

Jonathan couldn't think of a response. He wasn't even sure if that's what she wanted. Jocelyn just kept looking at his face, and no matter how much Jonathan wanted to look away or run out of the room he just stood there staring at her.

The silence between them stretched on for an eternity, at most it was probably only a couple of minutes, but the longer they stood there the more afraid Jonathan felt. He didn't want to admit it, but he was waiting for the rejection, for her to tell him to leave and never come back.

It took him a moment to notice the tears in her eyes. He opened his mouth to say something but his brain wasn't coming up with anything.

Jocelyn wasn't anything close to what he had imagined in his head. Jonathan had painted her as callous and uncaring to help himself deal with the fact she left him. He wanted to convince himself that he didn't want her either. He hadn't expected her to look at him like that.

Jocelyn looked away first, tilting her head down so she could wipe her eyes. "I suppose I should thank you for looking after your sister. Things didn't exactly go the way we thought they would." She sniffed and looked back up at him. "God, you should hear the way she talks about you. It's the same way she would talk about the superheroes in those movies she and Simon love."

Her words should have been comforting-and they were to a point, but they were also extremely upsetting.

"What did I do?" Jonathan was surprised by how small he sounded even to himself. Jocelyn looked confused. He couldn't look her in the eye when he elaborated, so he stared at the spot on the counter where her hand rested. "I've spent almost my entire life wondering what it was that I did. I mean I understand that the black eyes are unsettling, but I couldn't think of anything I could have done as a two-year-old that would make you leave me like that.

"I grew up watching Maryse Lightwood argue and get frustrated with her kids time after time, but at the end of the day it was like she hit a reset button. Nothing they did was bad enough that it made her stop loving them. _And they could talk back_." Jonathan had gotten louder the longer he spoke but his voice was audibly shaking. Tears stung at his own eyes. "So for years, I've been trying to figure out what I did that was bad enough to get _you_ to stop. I know our situation is nothing like the Lightwoods, not even close, but there had to be some part of you that wanted to save me, right?"

Jocelyn answered almost immediately, "If I had known there was any way, I would have. I was so young and so scared. I didn't know what he had done to you. I didn't know if I could fix it. Then I got pregnant again and your father—well you know what he's like—I ran out of time. I needed to do something. Jonathan, I _never_ thought he'd try to hurt you. He adored you." She was telling the truth. Jonathan felt sick to his stomach. Being something that earned Valentine's adoration wasn't something he could wear with a badge of honor.

Any other time he thought about this moment he was furious. He had never thought that he would get to this moment at all, and he definitely never thought that he would feel this vulnerable if he did. Jonathan took a deep breath and met his mother's eyes. "Please just tell me you aren't going to turn me away without getting to know me first."

"Those two years were the hardest of my life. I hated Valentine for doing this to you, and I hated myself for how I felt about you when you were just a baby." What she didn't say but implied was that she had hated him too. Jonathan felt like he was going to throw up. Jocelyn shook her head slowly, "Believe me, it wasn't anything you did. I was so scared of what you _might_ do. If I had known there would be a way to help you I would have done it."

Jonathan rubbed at his eyes, anything to stop them from getting blurrier. "I should hate you—I did hate you." His voice finally sounded steady. "No matter how you justify it, you abandoned me. I should hate you," He repeated.

Jocelyn looked down at her hands while he spoke to her. "I don't, not anymore," He confessed. He thought about what Magnus had told him. _I'm allowed to do things for me._ "I've put so much work into not being angry because I thought that meant I was giving into _that_ side of me. And if what I've been told is true, that's not the case. I deserve to be angry, and I am. I don't want my anger towards you to eat away at me, and I don't want it to ruin the relationship I have with Clary. I don't really know where to go from here." Jonathan chose his words carefully. He didn't want her thinking his motivations benefitted her.

Jocelyn let out a humorless laugh in response. "I don't really know either," She admitted.

"I do know it's important to Clary," Jonathan took a deep breath, "I'm willing to try and have some sort of relationship if you are. I don't know if I'm ready for all the mother and son stuff, so don't expect a card on Mother's day or anything like that."

"Mom!" Clary's voice rang out from the front of the house, "They gave us extra wontons because it took so long!"

Jocelyn wiped at her eyes one last time and cleared her throat. Jonathan made a similar effort to regain control of himself. It was difficult when his nerves felt so raw.

"Simon had to go home—Jon!" Clary nearly dropped the paper bag she was carrying, JOcleyn stepped forward and grabbed it before the food could fall to the floor. Clary jumped forward to wrap her arms around Jonathan's waist. "I'm so sorry about the other day, please don't be mad at me."

Jonathan rested his head on top of hers and patted her back. "I wasn't mad at you. Extremely irritated because of you? Sure." He looked up as Luke came into the room and set a plastic bag with the rest of the takeout on the counter. "Hey, how are you doing?"

Clary let go of Jonathan so she could hear his answer too. Luke shrugged it off. "I'm a little banged up but no worse for wear. I feel like I should be asking you that. You doing okay, kid?"

Jonathan glanced at Clary out of the corner of his eyes. She hadn't told them about Magnus's little procedure. He tucked his fists in his pocket and rocked back on his heels. Right now didn't seem like the time to get into it. "I'd say I've had worse, but I think we all know that's impossible."

"What made you decide to come over?" Clary asked from his side.

"I called him and invited him for dinner," Jocelyn chimed in. She opened one of the cabinets near her head and pulled out the stack of plates she had been putting away when he first arrived. "Here, Jonathan would you mind setting the table? Clary why don't you get everyone something to drink?"

Clary released her grip on Jonathan to get glasses, and Jonathan took the plates. "Guess we're getting right to the mundie stuff," He held up the plates to stress his point. "At the institute we usually just eat straight out of the cartons."

Jonathan took the plates over to the little round table on the other side of the cramped kitchen. "Chinese food doesn't seem like something shadowhunters would eat. Shouldn't you guys be more health conscious than that?" Clary brought over two glasses of soda and set them on the table.

"As you will learn, sometimes the only thing you want after patrol is sweet and sour chicken. Or in Jace's case moo Shu pork. Speaking of Jace have you talked to him recently?" Clary shot him a glare, "What? I have a right to know if something is going on there. He's my friend, well, kind of." Clary hit his arm with the back of her hand and shushed him.

He was missing something. He just wasn't sure what it was, not until Jocelyn chimed in. "Who's Jace?"

Clary answered too quickly to seem as nonchalant as she was going for, "He's just one of the other younger shadowhunters at the Institute. The Lightwoods adopted him after his parents died."

Jonathan froze half way through repositioning the two glasses Clary had set on the table. Jocelyn was staring at Clary expectantly and Clary was studiously avoiding acknowledging her stare. Giving up on getting further information from Clary, Jocelyn turned her look on Luke.

At that moment Luke was in the unique position of being the only person in the room that knew what was happening between Jocelyn and Clary, had met Jace, and was willing to speak. "Stephen and Celine's kid." It didn't sound like a stunning endorsement to Jonathan. In his opinion it felt a little unfair to reduce Jace to his parents especially with Jonathan's own issues in that area.

"He saved Clary's life multiple times," Jonathan offered in Jace's defense. "Jace was looking after her just as much as I was."

No one seemed to pay any attention to what he had to say. Clary pretended to be intensely interested in pouring two more glasses of soda, but Jocelyn didn't let up. "We're talking about this later," She said after she realized Clary wouldn't give up any more information.

"He's really not that bad," Jonathan tried again while Clary set the last to glasses on the table. She stepped on the toe of his boot probably to cause him pain but the steel tip prevented any damage. Jonathan smiled to himself at her attempt. "I'm trying to help," he whispered to her.

"Well stop it," She snapped back, "Mom's a little on the protective side."

"Yeah, I noticed. He says 'hi' by the way," Jonathan passed on, "Jace told me to tell you that when I left." The tops of Clary's cheeks turned pink as she slumped into the chair nearest to the refrigerator. Jonathan slid into the one next to her around the small table and bumped her arm with his. Alec did it to Izzy all the time when he wanted to let her know he was done teasing her for now. It felt good to have that moment with Clary.

It was ruined when Jocelyn and Luke set the boxes of takeout in the center of the table and took their own seats. So much of Jonathan's relationship with Clary had been built between them without adult supervision. It seemed weird to laugh and joke around with Jocelyn sitting there to witness it all. He wondered how long it would take for him to feel comfortable around his mother.

He didn't seem to be the only one out of his comfort zone. The kitchen was virtually silent except for the shuffle of takeout containers. Jonathan felt a little bit like an intruder. Clary said something about Simon when she had come in. He was taking Simon's spot at the dinner table. It was stupid for him to be jealous of the mundane boy, but he couldn't help it.

"So Clary," Luke began, "Are you set on living a shadowhunter life or are you going to think about it a little. I'm sure The Clave won't force you into anything considering all the work they would have to put into training you."

Clary picked at her fried rice with her chopsticks. "I was actually thinking about having Mom come with me to the institute when she was feeling better to arrange something with the Lightwoods?" Clary's eyes flickered up to Jocelyn. "I don't really know what it is that I don't know, so I figured you could sit down with them and figure something out for me? Like a training schedule or something."

"Oh god," Jocelyn paused with a piece of chicken halfway to her mouth, "I haven't talked to Maryse and Robert in years. I suppose I could go with you tomorrow if you aren't doing anything with Simon."

"The only problem is they might not have anyone to train you," Jonathan pointed out, "Hodge is in Clave custody. Most shadowhunters don't send their kids to American institutes to train so there wasn't much reason to have more than one tutor on staff with only four of us there."

"You could train me," Clary elbowed him, "You did a pretty good job the other day."

"You helped your sister train?" Jocelyn asked as she popped a piece of chicken in her mouth, "Maybe I should talk to Maryse about having you train her. I'd rather have someone a little more experienced make the lesson plans, but I think it would be good for the two of you."

"You want me to train Clary?" Jonathan was shocked. Training was a big deal. If Clary wasn't properly trained it could mean the difference between life and death. Jonathan didn't think he was ready for that responsibility.

Jocelyn shrugged and took a drink of her soda. "Most shadowhunter siblings grow up training together not training each other," She explained, "Still I think it would be a good bonding experience for the two of you. Think of it as the parts of your childhood you missed out on."

"My sister and I used to have so much fun training before we got to the academy," Luke said with a laugh. "She loved holding it over my head that I was bigger but she could take me down."

"I didn't know you had a sister," Clary chimed in.

Luke nodded like he had forgotten there was quite a bit Clary didn't know. "Yeah, we're going to have some catch up lessons for you aren't we?"

Jonathan thought back to when they were younger and Isabelle started to be allowed into training sessions with Alec. Alec complained about having her around but Jonathan knew he was always proud when Isabelle landed a punch or learned a new kick. It never seemed that important until now.

"Fine," He looked over at Clary, "But you better tell me the extent of your little defense training before we get started. I don't want any surprises this time." He held his fist up for her to knock her knuckles against.

"That's settled. We'll be over to the institute around noon is that good for you?" Jocelyn asked. "I don't want to intrude on anything."

Jonathan shrugged. He didn't have anything better to do. The Clave had put him on administrative leave for the next month. Jace and the Lightwoods only had to take two weeks but as soon as they were done he'd be stuck in his room bored out of his mind while they were on patrol. "I'd probably just be training anyway. And, hey, I can make it so Jace is around too and you can meet him—Ow!" This time Clary kicked him right in the shin underneath the table.

"Clarissa," Jocelyn warned before turning back to Jonathan. "I would love to meet Jace, and maybe after he could come with us and meet Luke for lunch down at the station. That would be fun right?" She smiled at Clary as if she were trying to say 'you're not getting out of this'.

Jonathan elbowed Clary, "Regret meeting me yet?" He smiled down at her.

"Starting to, you jerk." She reached over his plate to grab one of the containers. "You're in my way." Jonathan laughed and handed her the container. Having Clary there teasing him back was comforting.

Jonathan looked over at their mother. Jocelyn's expression looked similar to the one she had on when she saw Jonathan for the first time. Soft, and a little teary eyed, but she was definitely happy as she watched the two of them.

Clary had already moved onto pestering Luke about his sister and didn't notice how Jocelyn was looking at the two of them. Her eyes moved to look directly at Jonathan. He offered her a small smile that she returned gratefully. For the first time Jonathan allowed himself to consider the idea that Jocelyn had actually always wanted him. Maybe now they had a chance to have the relationship they both wanted.


End file.
